Methanotrophic carbon metabolism pathway genes and enzymes

ABSTRACT

Genes have been isolated from a Methylomonas sp encoding enzymes in the carbon flux pathway. The genes encode a 2-keto-3-deoxy-6-phosphogluconate (KDPGA) and a fructose bisphosphate aldolase (FFBPA), as well as numerous other genes. The genes will be useful in C1 metabolizing microorganisms for the manipulation of the carbon flux pathway.

This application is a division of application Ser. No. 09/934,901, filed Aug. 22, 2001, now U.S. Pat. No. 6,555,353, which claims the benefit of U.S. Provisional Application No. 60/229,906, filed Sep. 1, 2000.

FIELD OF THE INVENTION

The invention relates to the field of molecular biology and microbiology. More specifically, the invention relates to genes involved in the conversion of hexose sugars into 3-carbon metabolites in methanotrophic bacteria.

BACKGROUND OF THE INVENTION

Methanotrophic bacteria are defined by their ability to use methane as their sole source of carbon and energy. Although methanol is an obligate intermediate in the oxidation of methane, the ability to grow on methanol alone is highly variable among the obligate methanotrophs (Green, Peter. Taxonomy of Methylotrophic Bacteria. In: Methane and Methanol Utilizers (Biotechnology Handbooks 5) J. Colin Murrell and Howard Dalton eds. 1992 Pleanum Press NY. pp. 23-84)). The conversion of C1 compounds to complex molecules with C—C bonds is difficult and expensive by traditional chemical synthetic routes. Traditionally, methane is first converted to synthesis gas which is then used to produce other small molecular weight industrial precursors. The basic problem is activation of the methane molecule, a process which is thermodynamically very difficult to achieve by chemical means. Methanotrophs have proved useful mediators of this problem.

Methane monooxygenase is the enzyme required for the primary step in methane activation and the product of this reaction is methanol (Murrell et al., Arch. Microbiol. (2000), 173(5-6), 325-332). This remarkable reaction occurs at ambient temperatures and pressures, whereas chemical transformation of methane to methanol requires temperatures of hundreds of degrees and high pressures (Grigoryan, E. A., Kinet. Catal. (1999), 40(3), 350-363; WO 2000007718; U.S. Pat. No. 5,750,821). It is this ability to transform methane under ambient conditions, along with the abundance of methane, that makes the biotransformation of methane a potentially unique and valuable process.

The commercial applications of biotransformation of methane have historically fallen broadly into three categories: 1) Production of single cell protein, (Villadsen, John, Recent Trends Chem. React. Eng., [Proc. Int. Chem. React. Eng. Conf.], 2nd (1987), Volume 2, 320-33. Editor(s): Kulkami, B. D.; Mashelkar, R. A.; Sharma, M. M. Publisher Wiley East, New Delhi, India; Naguib, M., Proc. OAPEC Symp. Petroprotein, [Pap.] (1980), Meeting Date 1979, 253-77 Publisher: Organ. Arab Pet. Exporting Countries, Kuwait, Kuwait); 2) epoxidation of alkenes for production of chemicals (U.S. Pat. No. 4,348,476); and 3) biodegradation of chlorinated pollutants (Tsien et al., Gas, Oil, Coal, Environ. Biotechnol. 2, [Pap. Int. IGT Symp. Gas, Oil, Coal, Environ. Biotechnol.], 2nd (1990), 83-104, Editor(s): Akin, Cavit; Smith, Jared. Publisher: Inst. Gas Technol., Chicago, Ill.; WO 9633821; Merkley et al., Biorem. Recalcitrant Org., [Pap. Int. In Situ On-Site Bioreclam. Symp.], 3rd (1995), 165-74. Editor(s): Hinchee, Robert E; Anderson, Daniel B.; Hoeppel, Ronald E. Publisher Battelle Press, Columbus, Ohio; Meyer et al., Microb. Releases (1993), 2(1), 11-22). Only epoxidation of alkenes has experienced little commercial success due to low product yields, toxicity of products and the large amount of cell mass required to generate product.

Methanotrophic cells can further build the oxidation products of methane (i.e. formaldehyde) into more complex molecules such as protein, carbohydrate and lipids. For example, under certain conditions methanotrophs are known to produce exopolysaccharides (Ivanova et al., Mikrobiologiya (1988), 57(4), 600-5); Kilbane, John J., II Gas, Oil, Coal, Environ. Biotechnol. 3, [Pap. IGT's Int. Symp.], 3rd (1991), Meeting Date 1990, 207-26. Editor(s): Akin, Cavit; Smith, Jared. Publisher: IGT, Chicago, Ill.). Similarly, methanotrophs are known to accumulate both isoprenoid compounds and carotenoid pigments of various carbon lengths (Urakami et al., J. Gen. Appl. Microbiol. (1986), 32(4), 317-41). Although these compounds have been identified in methanotrophs, they have not been microbial platforms of choice for production because these organisms have very poorly developed genetic systems, thereby limiting metabolic engineering ability for chemicals.

A necessary prerequisite to metabolic engineering of methanotrophs is a full understanding, and optimization, of the carbon metabolism for maximum growth and/or product yield. In methanotrophic bacteria, methane is converted to biomolecules via a cyclic set of reactions known as the ribulose monophosphate pathway (RuMP) cycle. The RuMP pathway is comprised of three phases, each phase being a series of enzymatic steps. The first phase (fixation) is the aldol condensation of three molecules of C-1 (formaldehyde) with three molecules of pentose (ribulose-5-phospate) to form three molecules of a six-carbon sugar (fructose-6phosphate) catalyzed by hexulose monophosphate synthase. This fixation phase is common to all methylotrophic bacteria using the RuMP pathway.

The second phase is termed “cleavage” and results in splitting of that 6-carbon sugar into two 3-carbon molecules. This may be achieved via two possible routes. Fructose-6-phosphate is either converted into fructose-1,6-biphosphate (FBP) by phosphofructokinase, and subsquently cleaved by FBP aldolase (FBPA) to 3-carbon molecules, or oxidized to 2-keto-3-deoxy-6-phosphogluconate (KDPG) and ultimately cleaved to 3-carbon sugars by the enzyme catalyzed by KDPG aldolase. One of those 3-carbon molecules is recycled back through the RuMP pathway and the other 3-carbon fragment is utilized for cell growth.

In the third phase (the “rearrangement” phase), the regeneration of 3 molecules of ribulose-5phosphate is accomplished from the two remaining molecules of fructose-6-phosphate (from stage 1) and the one molecule of the 3-carbon sugar from stage 2. There are two possible routes to achieve the rearrangement. These routes in the rearrangement phase differ in that they involve either transaldolase (TA) or sedoheptulose-1,7-bisphosphatase (SBPase).

In methanotrophs and methylotrophs, the RuMP pathway may occur as one of three variants. These are the KDPGA/TA, FBPA/SBPase and FBPA/TA pathways. However, only two of these variants are commonly found. These two pathways are the FBPA/TA (fructose bisphophotase aldolase/Transaldolase) or the KDPGA/TA (keto deoxy phosphgogluconate aldolase/transaldolase) pathway, wherein only the FBPA/TA pathway is exergonic (Dijkhuizen et al. (1992) The Physiology and biochemistry of aerobic methanol-utilizing gram negative and gram positive bacteria. In: Methane and Methanol utilizers. P. 149-Coin Murrell and Howard Dalton, Plenum Press NY). Available literature suggests that obligatory methanotrophic bacteria such as Methylomonas rely solely on the KDPGA/TA pathway (Entner-Douderoff Pathway), while facultative methylotrophs utilize either the FBPA/SBPase or the FBPA/TA pathway (Dijkhuizen et al. supra). Energetically, this pathway is not as efficient as the Embden-Meyerhof pathway and thus could result in lower cellular production yields, as compared to organisms that do use the latter pathway. Therefore, a more energy efficient carbon processing pathway would greatly enhance the commercial viability of the methanotrophic platform for the generation of materials.

The problem to be solved therefore is to discover genes encoding a more energetically efficient carbon flux pathway that would enable a methanotrophic bacterial strain to better able to serve as a platform for the production of proteins and carbon containing materials. Applicants have solved the stated problem by providing the genes encoding the carbon flux pathway in a strain of Methylomonas. This pathway contains not only the expected elements of the Entner-Douderoff Pathway (including the 2-keto-3-deoxy-6-phosphogluconate aldolase) but additionally contains the elements of the more energy efficient Embden-Meyerhof pathway, containing the fructose-1,6-biphosphate aldolase. This discovery will permit the engineering of methanotrophs and other organisms for the energy efficient conversion of single carbon substrates such as methane and methanol to commercially useful products in the food and feed and materials industries.

SUMMARY OF THE INVENTION

The present invention provides an isolated nucleic acid molecule encoding a Methylomonas sp carbon flux enzyme, selected from the group consisting of:

(a) an isolated nucleic acid molecule encoding the amino acid sequence selected from the group consisting of SEQ ID NOs:2, 4, 6, 8, 10, 12, 14, 16,18, and 20;

(b) an isolated nucleic acid molecule that hybridizes with (a) under the following hybridization conditions: 0.1×SSC, 0.1% SDS, 65° C. and washed with 2×SSC, 0.1% SDS followed by 0.1×SSC, 0.1% SDS; and

(c) an isolated nucleic acid molecule that is complementary to (a) or (b).

Additionally the invention provides the gene products, encoded by the present invention and chimera made from the instant genes by operably linking the instant genes to suitable regulatory sequences. Similarly the invention provides transformed host cells expressing the instant genes or their chimera.

The invention additionally provides a method of obtaining a nucleic acid fragment encoding a carbon flux enzyme comprising:

(a) probing a genomic library with the nucleic acid fragment of the present invention;

(b) identifying a DNA clone that hybridizes with the nucleic acid fragment of the present invention; and

(c) sequencing the genomic fragment that comprises the clone identified in step (b),

wherein the sequenced genomic fragment encodes a carbon flux enzyme.

Alternatively the invention provides a method of obtaining a nucleic acid fragment encoding a carbon flux enzyme comprising:

(a) synthesizing at least one oligonucleotide primer corresponding to a portion of the sequence selected from the group consisting of SEQ ID NO:1, 3, 5, 7, 9, 11, 13, 15, 17, and 19;

(b) amplifying an insert present in a cloning vector using the oligonucleotide primer of step (a);

wherein the amplified insert encodes a portion of an amino acid sequence encoding a carbon flux enzyme.

In another embodiment the invention provides a method of altering carbon flow through a methanotrophic bacteria comprising, over-expressing at least one carbon flux gene selected from the group consisting of SEQ ID NO:1, 3, 5, 7, 9, 11, 13, 15, 17 and 19 in a methanotrophic strain such that the carbon flow is altered through the strain.

Additionally the invention provides a mutated gene encoding a carbon flux enzyme having an altered biological activity produced by a method comprising the steps of:

(i) digesting a mixture of nucleotide sequences with restriction endonucleases wherein said mixture comprises:

a) a native carbon flux gene;

b) a first population of nucleotide fragments which will hybridize to said native carbon flux gene;

c) a second population of nucleotide fragments which will not hybridize to said native carbon flux gene;

wherein a mixture of restriction fragments are produced;

(ii) denaturing said mixture of restriction fragments;

(iii) incubating the denatured said mixture of restriction fragments of step (ii) with a polymerase;

(iv) repeating steps (ii) and (iii) wherein a mutated carbon flux gene is produced encoding a protein having an altered biological activity.

BRIEF DESCRIPTION OF THE DRAWINGS, SEQUENCE DESCRIPTIONS AND BIOLOGICAL DEPOSITS

FIG. 1 is a schematic showing the enzyme catalyzed reaction of the Embden-Meyerhof and the Entner-Douderoff carbon pathways present in the Methylomonas 16a strain.

The invention can be more fully understood from the following detailed description and the accompanying sequence descriptions which form a part of this application.

The following sequence descriptions and sequences listings attached hereto comply with the rules governing nucleotide and/or amino acid sequence disclosures in patent applications as set forth in 37 C.F.R. §1.821-1.825. The Sequence Descriptions contain the one letter code for nucleotide sequence characters and the three letter codes for amino acids as defined in conformity with the IUPAC-IYUB standards described in Nucleic Acids Research 13:3021-3030 (1985) and in the Biochemical Journal 219 (No. 2), 345-373 (1984) which are herein incorporated by reference. The symbols and format used for nucleotide and amino acid sequence data comply with the rules set forth in 37 C.F.R. §1.822.

SEQ ID SEQ ID Description Nucleic acid Peptide Transaldolase: Carbon Flux 1 2 Transaldolase: Carbon Flux 3 4 Fructose bisphosphate aldoslase: Carbon Flux 5 6 Fructose bisphosphate aldoslase: Carbon Flux 7 8 KHG/KDPG Aldolase: Carbon Flux 9 10 Phosphoglucomutase: carbon Flux 11 12 Glucose 6 phosphate isomerase: Carbon flux 13 14 Phosphofructokinase pyrophosphate dependent: 15 16 Carbon Flux 6-Phosphogluconate dehydratase: Carbon flux 17 18 Glucose 6 phosphate 1 dehydrogenase: Carbon 19 20 Flux

Applicants made the following biological deposits under the terms of the Budapest Treaty on the Intemational Recognition of the Deposit of Micro-organisms for the Purposes of Patent Procedure:

Depositor Identification International Depository Reference Designation Date of Deposit Methylomonas 16a ATCC PTA 2402 August 22, 2000

DETAILED DESCRIPTION OF THE INVENTION

The invention relates to genes encoding enzymes in the carbon flux pathway from a methanotrophic bacteria. The pathway contains genes encoding fructose-1,6-biphosphate aldolase (FBP aldolase) and a pyrophosphate dependent phosphofructokinase pyrophosphate which are indicative of the Embden-Meyerhof pathway typically not found in methanotrophs. The Embden-Meyerhof pathway is energetically more favorable than the carbon flux pathway typically associated with these organisms. Additionally the invention provides genes encoding elements of the Entner-Douderoff Pathway, which is typically found in methanotrophic bacteria. These genes include 6-Phosphogluconate dehydratase, a glucose-6-phosphate-1-dehydrogenase, and a 2-keto-3-deoxy-6phosphogluconate aldolase. Common to both pathways are new genes encoding a transaldolase and a phosphoglucomutase. Knowledge of the sequence of the present genes will be useful for altering the carbon flow in methanotrophs and other bacteria resulting in more productive bacterial fermentation platforms for the production of chemicals and food and feed products.

In this disclosure, a number of terms and abbreviations are used. The following definitions are provided.

“Open reading frame” is abbreviated ORF.

“Polymerase chain reaction” is abbreviated PCR.

The term “a C1 carbon substrate” refers to any carbon-containing molecule that lacks a carbon-carbon bond. Examples are methane, methanol, formaldehyde, formic acid, methylated amines, methylated thiols.

The term “RuMP” is the abbreviation for ribulose monophosphate and the “RuMP pathway” refers to the set of enzymes found in methanotrophic bacteria responsible of the conversion of the methane monooxygenase product (methanol, formaldehyde) to three carbon moieties useful for energy production in the methanotroph.

The term “Embden-Meyerhof pathway” refers to the series of biochemical reactions for conversion of hexoses such as glucose and fructose to important cellular 3-carbon intermediates such as glyceraldehyde 3 phosphate, dihydroxyacetone phosphate, phosphoenol pyruvate and pyruvate. These reactions typically proceed with net yield of biochemically useful energy in the form of ATP. The key enzymes unique to the Embden-Meyerhof pathway are the phosphofructokinase and fructose 1,6 bisphosphate aldolase.

The term “Entner-Douderoff pathway” refers to a series of biochemical reactions for conversion of hexoses such as as glucose or fructose to the important 3-carbon cellular intermediates pyruvate and glyceraldehyde 3 phosphate, without any net production of biochemically useful energy. The key enzymes unique to the Entner-Douderoff pathway are the 6 phosphogluconate dehydratase and the ketodeoxyphosphogluconate aldolase.

The term “high growth methanotrophic bacterial strain” refers to a bacterium capable of growth with methane or methanol as the sole carbon and energy source and which possesses a functional Embden-Meyerhof carbon flux pathway resulting in yield of cell mass per gram of C1 substrate metabolized. The specific “high growth methanotrophic bacterial strain” described herein is referred to as “Methylomonas 16a” or “16a”, which terms are used interchangeably.

The term “methanotroph” or “methanotrophic bacteria” will refer to a prokaryotic microorganism capable of utilizing methane as its primary carbon and energy source.

As used herein, an “isolated nucleic acid fragment” is a polymer of RNA or DNA that is single- or double-stranded, optionally containing synthetic, non-natural or altered nucleotide bases. An isolated nucleic acid fragment in the form of a polymer of DNA may be comprised of one or more segments of cDNA, genomic DNA or synthetic DNA.

The term “carbon flux gene” will refer to any gene encoding an enzyme that functions to convert C1 substrates in methanotrophic bacteria to metabolically useful products. As used herein “carbon flux genes” will be those encoding a phosphoglucomutase, a transaldolase, a glucose-6-phosphate isomerase, a phosphofructokinase (pyrophosphate dependent), a 6-Phosphogluconate dehydratase, and a glucose 6 phosphate 1 dehydrogenase, as well as the distinctive fructose bisphosphate aldolase and keto deoxy phosphogluconate aldolase.

“Carbon Flux enzymes” will refer to the gene products of the carbon flux genes.

The term “transaldolase” will be abbrevaited “TA” and will refer to an enzyme that catalyzes the reaction of sedoheptulose 7-phosphate and D-glyceraldehyde 3-phosphate to give D-erythrose 4-phosphate and D-fructose 6-phosphate

The term “fructose bisphosphate aldolase” will be abbreviated “FFBPA” and will refer to an enzyme that catalyzes the reaction of D-fructose 1,6-bisphosphate to give glycerone-phosphate and D-glyceraldehyde 3-phosphate.

The term “keto deoxy phosphogluconate aldolase” will be abbreviated “KDPGA” and will refer to an enzyme that catalyzes the reaction of 2-dehydro-3-deoxy-d-gluconate 6-phosphate to give pyruvate and D-glyceraldehyde 3-phosphate.

The term “phosphoglucomutase” and will refer to an enzyme that catalyzes the interconversion of glucose-6-phosphate to glucose-1-phosphate.

The term “glucose-6-phosphate isomerase” and will refer to an enzyme that catalyzes the conversion of fructose-6-phosphate to glucose-6-phosphate.

The term “phosphofructokinase” and will refer to an enzyme that catalyzes the conversion of fructose-6-phosphate to fructose-1,6-bisphosphate.

The term “6-phosphogluconate dehydratase” and will refer to an enzyme that catalyzes the conversion of 6-phosphogluconate to 2-keto-3-deoxy-6phosphogluconate (KDPG).

The term “6-phosphogluconate-6-phosphate-1 dehydrogenase” and will refer to an enzyme that catalyzes the conversion of glucose-6-phosphate to 6-phosphogluconate.

As used herein, “substantially similar” refers to nucleic acid fragments wherein changes in one or more nucleotide bases results in substitution of one or more amino acids, but do not affect the functional properties of the protein encoded by the DNA sequence. “Substantially similar” also refers to nucleic acid fragments wherein changes in one or more nucleotide bases does not affect the ability of the nucleic acid fragment to mediate alteration of gene expression by antisense or co-suppression technology. “Substantially similar” also refers to modifications of the nucleic acid fragments of the instant invention such as deletion or insertion of one or more nucleotide bases that do not substantially affect the functional properties of the resulting transcript. It is therefore understood that the invention encompasses more than the specific exemplary sequences.

For example, it is well known in the art that alterations in a gene which result in the production of a chemically equivalent amino acid at a given site, but do not effect the functional properties of the encoded protein are common. For the purposes of the present invention substitutions are defined as exchanges within one of the following five groups:

1. Small aliphatic, nonpolar or slightly polar residues: Ala, Ser, Thr (Pro, Gly);

2. Polar, negatively charged residues and their amides: Asp, Asn, Glu, Gln;

3. Polar, positively charged residues: His, Arg, Lys;

4. Large aliphatic, nonpolar residues: Met, Leu, Ile, Val (Cys); and

5. Large aromatic residues: Phe, Tyr, Trp.

Thus, a codon for the amino acid alanine, a hydrophobic amino acid, may be substituted by a codon encoding another less hydrophobic residue (such as glycine) or a more hydrophobic residue (such as valine, leucine, or isoleucine). Similarly, changes which result in substitution of one negatively charged residue for another (such as aspartic acid for glutamic acid) or one positively charged residue for another (such as lysine for arginine) can also be expected to produce a functionally equivalent product.

In many cases, nucleotide changes which result in alteration of the N-terminal and C-terminal portions of the protein molecule would also not be expected to alter the activity of the protein.

Each of the proposed modifications is well within the routine skill in the art, as is determination of retention of biological activity of the encoded products. Moreover, the skilled artisan recognizes that substantially similar sequences encompassed by this invention are also defined by their ability to hybridize, under stringent conditions (0.1×SSC, 0.1% SDS, 65° C. and washed with 2×SSC, 0.1% SDS followed by 0.1×SSC, 0.1% SDS), with the sequences exemplified herein. Preferred substantially similar nucleic acid fragments of the instant invention are those nucleic acid fragments whose DNA sequences are at least 80% identical to the DNA sequence of the nucleic acid fragments reported herein. More preferred nucleic acid fragments are at least 90% identical to the DNA sequence of the nucleic acid fragments reported herein. Most preferred are nucleic acid fragments that are at least 95% identical to the DNA sequence of the nucleic acid fragments reported herein.

A nucleic acid molecule is “hybridizable” to another nucleic acid molecule, such as a cDNA, genomic DNA, or RNA, when a single stranded form of the nucleic acid molecule can anneal to the other nucleic acid molecule under the appropriate conditions of temperature and solution ionic strength. Hybridization and washing conditions are well known and exemplified in Sambrook, J., Fritsch, E. F. and Maniatis, T. Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor (1989), particularly Chapter 11 and Table 11.1 therein (entirely incorporated herein by reference). The conditions of temperature and ionic strength determine the “stringency” of the hybridization. Stringency conditions can be adjusted to screen for moderately similar fragments, such as homologous sequences from distantly related organisms, to highly similar fragments, such as genes that duplicate functional enzymes from closely related organisms. Post-hybridization washes determine stringency conditions. One set of preferred conditions uses a series of washes starting with 6×SSC, 0.5% SDS at room temperature for 15 min, then repeated with 2×SSC, 0.5% SDS at 45° C. for 30 min, and then repeated twice with 0.2×SSC, 0.5% SDS at 50° C. for 30 min. A more preferred set of stringent conditions uses higher temperatures in which the washes are identical to those above except for the temperature of the final two 30 min washes in 0.2×SSC, 0.5% SDS was increased to 60° C. Another preferred set of highly stringent conditions uses two final washes in 0.1×SSC, 0.1% SDS at 65° C. Hybridization requires that the two nucleic acids contain complementary sequences, although depending on the stringency of the hybridization, mismatches between bases are possible. The appropriate stringency for hybridizing nucleic acids depends on the length of the nucleic acids and the degree of complementation, variables well known in the art. The greater the degree of similarity or homology between two nucleotide sequences, the greater the value of Tm for hybrids of nucleic acids having those sequences. The relative stability (corresponding to higher Tm) of nucleic acid hybridizations decreases in the following order: RNA:RNA, DNA:RNA, DNA:DNA. For hybrids of greater than 100 nucleotides in length, equations for calculating Tm have been derived (see Sambrook et al., supra, 9.50-9.51). For hybridizations with shorter nucleic acids, i.e., oligonucleotides, the position of mismatches becomes more important, and the length of the oligonucleotide determines its specificity (see Sambrook et al., supra, 11.7-11.8). In one embodiment the length for a hybridizable nucleic acid is at least about 10 nucleotides. Preferable a minimum length for a hybridizable nucleic acid is at least about 15 nucleotides; more preferably at least about 20 nucleotides; and most preferably the length is at least 30 nucleotides. Furthermore, the skilled artisan will recognize that the temperature and wash solution salt concentration may be adjusted as necessary according to factors such as length of the probe.

A “substantial portion” of an amino acid or nucleotide sequence comprising enough of the amino acid sequence of a polypeptide or the nucleotide sequence of a gene to putatively identify that polypeptide or gene, either by manual evaluation of the sequence by one skilled in the art, or by computer-automated sequence comparison and identification using algorithms such as BLAST (Basic Local Alignment Search Tool; Altschul, S. F., et al., (1993) J. Mol. Biol. 215:403410; see also www.ncbi.nlm.nih.gov/BLAST/). In general, a sequence of ten or more contiguous amino acids or thirty or more nucleotides is necessary in order to putatively identify a polypeptide or nucleic acid sequence as homologous to a known protein or gene. Moreover, with respect to nucleotide sequences, gene specific oligonucleotide probes comprising 20-30 contiguous nucleotides may be used in sequence-dependent methods of gene identification (e.g., Southern hybridization) and isolation (e.g., in situ hybridization of bacterial colonies or bacteriophage plaques). In addition, short oligonucleotides of 12-15 bases may be used as amplification primers in PCR in order to obtain a particular nucleic acid fragment comprising the primers. Accordingly, a “substantial portion” of a nucleotide sequence comprises enough of the sequence to specifically identify and/or isolate a nucleic acid fragment comprising the sequence. The instant specification teaches partial or complete amino acid and nucleotide sequences encoding one or more particular microbial proteins. The skilled artisan, having the benefit of the sequences as reported herein, may now use all or a substantial portion of the disclosed sequences for purposes known to those skilled in this art. Accordingly, the instant invention comprises the complete sequences as reported in the accompanying Sequence Listing, as well as substantial portions of those sequences as defined above.

The term “complementary” is used to describe the relationship between nucleotide bases that are capable to hybridizing to one another. For example, with respect to DNA, adenosine is complementary to thymine and cytosine is complementary to guanine. Accordingly, the instant invention also includes isolated nucleic acid fragments that are complementary to the complete sequences as reported in the accompanying Sequence Listing as well as those substantially similar nucleic acid sequences.

The term “percent identity”, as known in the art, is a relationship between two or more polypeptide sequences or two or more polynucleotide sequences; as determined by comparing the sequences. In the art, “identity” also means the degree of sequence relatedness between polypeptide or polynucleotide sequences, as the case may be, as determined by the match between strings of such sequences. “Identity” and “similarity” can be readily calculated by known methods, including but not limited to those described in: Computational Molecular Biology (Lesk, A. M., ed.) Oxford University Press, New York (1988); Biocomputing: Informatics and Genome Projects (Smith, D. W., ed.) Academic Press, New York (1993); Computer Analysis of Sequence Data, Part I (Griffin, A. M., and Griffin, H. G., eds.) Humana Press, New Jersey (1994); Sequence Analysis in Molecular Biology (von Heinje, G., ed.) Academic Press (1987); and Sequence Analysis Primer (Gribskov, M. and Devereux, J., eds.) Stockton Press, NY (1991). Preferred methods to determine identity are designed to give the best match between the sequences tested. Methods to determine identity and similarity are codified in publicly available computer programs. Sequence alignments and percent identity calculations may be performed using the Megalign program of the LASERGENE bioinformatics computing suite (DNASTAR Inc., Madison, Wis.). Multiple alignment of the sequences was performed using the Clustal method of alignment (Higgins and Sharp (1989) CABIOS. 5:151-153) with the default parameters (GAP PENALTY=10, GAP LENGTH PENALTY=10). Default parameters for pairwise alignments using the Clustal method were KTUPLE 1, GAP PENALTY=3, WINDOW=5 and DIAGONALS SAVED=5.

Suitable nucleic acid fragments (isolated polynucleotides of the present invention) encode polypeptides that are at least about 70% identical, preferably at least about 80% identical to the amino acid sequences reported herein. Preferred nucleic acid fragments encode amino acid sequences that are about 85% identical to the amino acid sequences reported herein. More preferred nucleic acid fragments. encode amino acid sequences that are at least about 90% identical to the amino acid sequences reported herein. Most preferred are nucleic acid fragments that encode amino acid sequences that are at least about 95% identical to the amino acid sequences reported herein. Suitable nucleic acid fragments not only have the above homologies but typically encode a polypeptide having at least 50 amino acids, preferably at least 100 amino acids, more preferably at least 150 amino acids, still more preferably at least 200 amino acids, and most preferably at least 250 amino acids.

“Codon degeneracy” refers to the nature in the genetic code permitting variation of the nucleotide sequence without effecting the amino acid sequence of an encoded polypeptide. Accordingly, the instant invention relates to any nucleic acid fragment that encodes all or a substantial portion of the amino acid sequence encoding the instant microbial polypeptides as set forth in SEQ ID NOs:2, 4, 6, 8, and 10. The skilled artisan is well aware of the “codon-bias” exhibited by a specific host cell in usage of nucleotide codons to specify a given amino acid. Therefore, when synthesizing a gene for improved expression in a host cell, it is desirable to design the gene such that its frequency of codon usage approaches the frequency of preferred codon usage of the host cell.

“Synthetic genes” can be assembled from oligonucleotide building blocks that are chemically synthesized using procedures known to those skilled in the art. These building blocks are ligated and annealed to form gene segments which are then enzymatically assembled to construct the entire gene. “Chemically synthesized”, as related to a sequence of DNA, means that the component nucleotides were assembled in vitro. Manual chemical synthesis of DNA may be accomplished using well-established procedures, or automated chemical synthesis can be performed using one of a number of commercially available machines. Accordingly, the genes can be tailored for optimal gene expression based on optimization of nucleotide sequence to reflect the codon bias of the host cell. The skilled artisan appreciates the likelihood of successful gene expression if codon usage is biased towards those codons favored by the host. Determination of preferred codons can be based on a survey of genes derived from the host cell where sequence information is available.

“Gene” refers to a nucleic acid fragment that expresses a specific protein, including regulatory sequences preceding (5′ non-coding sequences) and following (3′ non-coding sequences) the coding sequence. “Native gene” refers to a gene as found in nature with its own regulatory sequences “Chimeric gene” refers to any gene that is not a native gene, comprising regulatory and coding sequences that are not found together in nature. Accordingly, a chimeric gene may comprise regulatory sequences and coding sequences that are derived from different sources, or regulatory sequences and coding sequences derived from the same source, but arranged in a manner different than that found in nature. “Endogenous gene” refers to a native gene in its natural location in the genome of an organism. A “foreign” gene refers to a gene not normally found in the host organism, but that is introduced into the host organism by gene transfer. Foreign genes can comprise native genes inserted into a non-native organism, or chimeric genes. A “transgene” is a gene that has been introduced into the genome by a transformation procedure.

“Coding sequence” refers to a DNA sequence that codes for a specific amino acid sequence. “Suitable regulatory sequences” refer to nucleotide sequences located upstream (5′ non-coding sequences), within, or downstream (3′ non-coding sequences) of a coding sequence, and which influence the transcription, RNA processing or stability, or translation of the associated coding sequence. Regulatory sequences may include promoters, translation leader sequences, introns, polyadenylation recognition sequences, RNA processing site, effector binding site and stem-loop structure.

“Promoter” refers to a DNA sequence capable of controlling the expression of a coding sequence or functional RNA. In general, a coding sequence is located 3′ to a promoter sequence. Promoters may be derived in their entirety from a native gene, or be composed of different elements derived from different promoters found in nature, or even comprise synthetic DNA segments. It is understood by those skilled in the art that different promoters may direct the expression of a gene in different tissues or cell types, or at different stages of development, or in response to different environmental or physiological conditions. Promoters which cause a gene to be expressed in most cell types at most times are commonly referred to as “constitutive promoters”. It is further recognized that since in most cases the exact boundaries of regulatory sequences have not been completely defined, DNA fragments of different lengths may have identical promoter activity.

The “3′ non-coding sequences” refer to DNA sequences located downstream of a coding sequence and include polyadenylation recognition sequences and other sequences encoding regulatory signals capable of affecting mRNA processing or gene expression. The polyadenylation signal is usually characterized by affecting the addition of polyadenylic acid tracts to the 3′ end of the mRNA precursor.

“RNA transcript” refers to the product resulting from RNA polymerase-catalyzed transcription of a DNA sequence. When the RNA transcript is a perfect complementary copy of the DNA sequence, it is referred to as the primary transcript or it may be an RNA sequence derived from post-transcriptional processing of the primary transcript and is referred to as the mature RNA. “Messenger RNA (mRNA)” refers to the RNA that is without introns and that can be translated into protein by the cell. “cDNA” refers to a double-stranded DNA that is complementary to and derived from mRNA. “Sense” RNA refers to RNA transcript that includes the mRNA and so can be translated into protein by the cell. “Antisense RNA” refers to a. RNA transcript that is complementary to all or part of a target primary transcript or mRNA and that blocks the expression of a target gene (U.S. Pat. No. 5,107,065;WO 9928508). The complementarity of an antisense RNA may be with any part of the specific gene transcript, i.e., at the 5′ non-coding sequence, 3′ non-coding sequence, or the coding sequence. “Functional RNA” refers to antisense RNA, ribozyme RNA, or other RNA that is not translated yet has an effect on cellular processes.

The term “operably linked” refers to the association of nucleic acid sequences on a single nucleic acid fragment so that the function of one is affected by the other. For example, a promoter is operably linked with a coding sequence when it is capable of affecting the expression of that coding sequence (i.e., that the coding sequence is under the transcriptional control of the promoter). Coding sequences can be operably linked to regulatory sequences in sense or antisense orientation.

The term “expression”, as used herein, refers to the transcription and stable accumulation of sense (mRNA) or antisense RNA derived from the nucleic acid fragment of the invention. Expression may also refer to translation of mRNA into a polypeptide.

“Transformation” refers to the transfer of a nucleic acid fragment into the genome of a host organism, resulting in genetically stable inheritance. Host organisms containing the transformed nucleic acid fragments are referred to as “transgenic” or “recombinant” or “transformed” organisms.

The terms “plasmid”, “vector” and “cassette” refer to an extra chromosomal element often carrying genes which are not part of the central metabolism of the cell, and usually in the form of circular double-stranded DNA molecules. Such elements may be autonomously replicating sequences. genome integrating sequences, phage or nucleotide sequences, linear or circular, of a single- or double-stranded DNA or RNA, derived from any source, in which a number of nucleotide sequences have been joined or recombined into a unique construction which is capable of introducing a promoter fragment and DNA sequence for a selected gene product along with appropriate 3′ untranslated sequence into a cell. “Transformation cassette” refers to a specific vector containing a foreign gene and having elements in addition to the foreign gene that facilitate transformation of a particular host cell. “Expression cassette” refers to a specific vector containing a foreign gene and having elements in addition to the foreign gene that allow for enhanced expression of that gene in a foreign host.

The term “altered biological activity” will refer to an activity, associated with a protein encoded by a microbial nucleotide sequence which can be measured by an assay method, where that activity is either greater than or less than the activity associated with the native microbial sequence. “Enhanced biological activity” refers to an altered activity that is greater than that associated with the native sequence. “Diminished biological activity” is an altered activity that is less than that associated with the native sequence.

The term “sequence analysis software” refers to any computer algorithm or software program that is useful for the analysis of nudeotide or amino acid sequences. “Sequence analysis software” may be commercially available or independently developed. Typical sequence analysis software will include but is not limited to the GCG suite of programs (Wisconsin Package Version 9.0, Genetics Computer Group (GCG), Madison, Wis.), BLASTP, BLASTN, BLASTX (Altschul et al., J. Mol. Biol. 215:403-410 (1990), and DNASTAR (DNASTAR, Inc. 1228 S. Park St. Madison, Wis. 53715 USA), and the FASTA program incorporating the Smith-Waterman algorithm (W. R. Pearson, Comput. Methods Genome Res., [Proc. Int. Symp.] (1994), Meeting Date 1992, 111-20. Editor(s): Suhai, Sandor. Publisher: Plenum, New York, N.Y.). Within the context of this application it will be understood that where sequence analysis software is used for analysis, that the results of the analysis will be based on the “default values” of the program referenced, unless otherwise specified. As used herein “default values” will mean any set of values or parameters which originally load with the software when first initialized.

Standard recombinant DNA and molecular cloning techniques used here are well known in the art and are described by Sambrook, J., Fritsch, E. F. and Maniatis, T., Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (1989) (hereinafter “Maniatis”); and by Silhavy, T. J., Bennan, M. L. and Enquist, L. W., Experiments with Gene Fusions, Cold Spring Harbor Laboratory Cold Press Spring Harbor, N.Y. (1984); and by Ausubel, F. M. et al., Current Protocols in Molecular Biology, published by Greene Publishing Assoc. and Wiley-Interscience (1987).

The invention provides genes and gene products involved in the carbon flux pathway of a Methylomonas sp. The invention alternatively provides methods of altering carbon flux in a methanotrophic bacteria comprising the up-regulation or down-regulation of carbon flux either by introducing the present genes into a host or by suppressing the expression of sequence homologs to the present genes.

Isolation of Methylomonas 16a

The original environmental sample containing Methylomonas 16a was obtained from pond sediment. The pond sediment was inoculated directly into a defined mineral medium under 25% methane in air. Methane was used as the sole source of carbon and energy. Growth was followed until the optical density at 660 nm was stable, whereupon the culture was transferred to fresh medium such that a 1:100 dilution was achieved. After 3 successive transfers with methane as the sole carbon and energy source, the culture was plated onto defined minimal medium agar and incubated under 25% methane in air. Many methanotrophic bacterial species were isolated in this manner. However, Methylomonas 16a was selected as the organism to study due to the rapid growth of colonies, large colony size, its ability to grow on minimal media, and pink pigmentation indicative of an active biosynthetic pathway for carotenoids.

Methanotrophs are classified into three metabolic groups (“Type I”, “Type X” or “Type II”) based on the mode of carbon incorporation, morphology, % GC content and the presence or absence of key specific enzymes. Example 4, Table 2 shows key traits determined for Methylomonas 16a in relation to the three major groupings of methanotrophs. The strain clearly falls into the Type I grouping based on every trait, with the exception of nitrogen fixation. Available literature suggests that these organisms do not fix nitrogen. Therefore, Methylomonas 16a appears to be unique in this aspect of nitrogen metabolism.

16SrRNA extracted from the strain was sequenced and compared to known 16SrRNAs from other microorganisms. The data showed 96% identity to sequences from Methylomonas sp. KSP III and Methylomonas sp. Strain LW13. Based on this evidence, as well as the other physiological traits described in Table 2, it was concluded that the strain was a member of the genus Methylomonas.

The present sequences have been identified by comparison of random cDNA sequences to the GenBank database using the BLAST algorithms well known to those skilled in the art. The nucleotide sequence of two genes encoding fructose bisphosphate aldolase (FFBPA) have been identified. The gene sequences for these genes are given in SEQ ID NO:5 and SEQ ID NO:7. The corresponding gene products are given in SEQ ID NO:6 and SEQ ID NO:8. Similarly, two genes encoding a transaldolase associated with the carbon flux pathway have been identified. These genes are set forth in SEQ ID NO:1 and SEQ ID NO:3. Their corresponding gene products are set forth in SEQ ID NO:2 and SEQ ID NO:4. Additionally a gene encoding a keto deoxy phosphogluconate aldolase (KDPGA) has been identified and is given in SEQ ID NO:9 and the deduced amino acid sequence of the gene product is given in SEQ ID NO:10.

Genes encoding a phosphoglucomutase have also been identified where the genes and the corresponding gene products are given as SEQ ID NOs:11 and 12, respectively. Similarly, genes and gene products have been identified encoding a glucose 6 phosphate isomerase where the genes and their corresponding gene products are given as SEQ ID NO:13 and 14, respectively. Genes encoding a phosphofructokinase have also been identified where the genes and gene products are given as SEQ ID NOs:15 and 16, respectively. A 6-phosphogluconate dehydratase encoding gene has been identified and the gene and gene product are given in SEQ ID NOs:17 and 18, respectively. Another carbon flux enzyme, 6-phosphogluconate 6 phosphate 1 dehydrogenase, has been identified and the gene and gene product is given in SEQ ID NOs:19 and 20, respectively.

Accordingly, the present invention provides a Methylomonas sp having a gene encoding a fructose bisphosphate aldolase (FBP aldolase), a keto deoxy phosphgogluconate/transaldolase (KDPG aldolase), a phosphoglucomutase, a glucose 6 phosphate isomerase, a phosphofructokinase, a 6-phosphogluconate dehydratase, and a 6-phosphogluconate-6-phosphate 1 dehydrogenase.

More specifically the present strain is recognized as having a gene encoding an transaldolase having about 78% identity at the amino acid level over length of 328 amino acids using a Smith-Waterman alignment algorithm (W. R. Pearson, Comput. Methods Genome Res., [Proc. Int. Symp.] (1994), Meeting Date 1992, 111-20. Editor(s): Suhai, Sandor. Publisher: Plenum, New York, N.Y.) to the sequence set forth in SEQ ID NO:2. More preferred amino acid fragments are at least about 80%-90% identical to the sequences herein. Most preferred are nucleic acid fragments that are at least 95% identical to the amino acid fragments reported herein. Similarly, preferred transaldolase encoding nucleic acid sequences corresponding to the instant seqeunces are those encoding active proteins and which are at least 80% identical to the nucleic acid sequences of reported herein. More preferred transaldolase nucleic acid fragments are at least 90% identical to the sequences herein. Most preferred are transaldolase nucleic acid fragments that are at least 95% identical to the nucleic acid fragments reported herein.

More specifically the present strain is recognized as having a gene encoding an transaldolase having about 50% identity at the amino acid level over length of 160 amino acids using a Smith-Waterman alignment algorithm (W. R. Pearson, supra) to the sequence set forth in SEQ ID NO:4. More preferred amino acid fragments are at least about 80%-90% identical to the sequences herein. Most preferred are nucleic acid fragments that are at least 95% identical to the amino acid fragments reported herein. Similarly, preferred transaldolase encoding nucleic acid sequences corresponding to the instant seqeunces are those encoding active proteins and which are at least 80% identical to the nucleic acid sequences of reported herein. More preferred transaldolase nucleic acid fragments are at least 90% identical to the sequences herein. Most preferred are transaldolase nucleic acid fragments that are at least 95% identical to the nucleic acid fragments reported herein.

Additionally the present strain is recognized as having a gene encoding an FBP aldolase having about 76% identity at the amino acid level over length of 335 amino acids using a Smith-Waterman alignment algorithm (W. R. Pearson, supra) to the sequence set forth in SEQ ID NO:6. More preferred amino acid fragments are at least about 80%-90% identical to the sequences herein. Most preferred are nucleic acid fragments that are at least 95% identical to the amino acid fragments reported herein. Similarly, preferred FBP aldolase encoding nucleic acid sequences corresponding to the instant seqeunces are those encoding active proteins and which are at least 80% identical to the nucleic acid sequences of reported herein. More preferred FBP aldolase nucleic acid fragments are at least 90% identical to the sequences herein. Most preferred are FBP aldolase nucleic acid fragments that are at least 95% identical to the nucleic acid fragments reported herein.

Additionally the present strain is recognized as having a gene encoding an FBP aldolase having about 40% identity at the amino acid level over length of 358 amino acids using a Smith-Waterman alignment algorithm (W. R. Pearson, supra) to the sequence set forth in SEQ ID NO:8. More preferred amino acid fragments are at least about 80%-90% identical to the sequences herein. Most preferred are nudeic acid fragments that are at least 95% identical to the amino acid fragments reported herein. Similarly, preferred FBP aldolase encoding nucleic acid sequences corresponding to the instant seqeunces are those encoding active proteins and which are at least 80% identical to the nucleic acid sequences of reported herein. More preferred FBP aldolase nucleic acid fragments are at least 90% identical to the sequences herein. Most preferred are FBP aldolase nucleic acid fragments that are at least 95% identical to the nucleic acid fragments reported herein.

Additionally the present strain is recognized as having a gene encoding an KDPG aldolase having about 59% identity at the amino acid level over length of 212 amino acids using a Smith-Waterman alignment algorithm (W. R. Pearson, supra) to the sequence set forth in SEQ ID NO:10. More preferred amino acid fragments are at least about 80%-90% identical to the sequences herein. Most preferred are nucleic acid fragments that are at least 95% identical to the amino acid fragments reported herein. Similarly, preferred KDPG aldolase encoding nucleic acid sequences corresponding to the instant seqeunces are those encoding active proteins and which are at least 80% identical to the nucleic acid sequences of reported herein. More preferred KDPG aldolase nucleic acid fragments are at least 90% identical to the sequences herein. Most preferred are KDPG aldolase nucleic acid fragments that are at least 95% identical to the nucleic acid fragments reported herein.

Additionally the present strain is recognized as having a gene encoding an phosphoglucomutase having about 65% identity at the amino acid level over length of 545 amino acids using a Smith-Waterman alignment algorithm (W. R. Pearson, supra) to the sequence set forth in SEQ ID NO:12. More preferred amino acid fragments are at least about 80%-90% identical to the sequences herein. Most preferred are nucleic acid fragments that are at least 95% identical to the amino acid fragments reported herein. Similarly, preferred phosphoglucomutase encoding nucleic acid sequences corresponding to the instant seqeunces are those encoding active proteins and which are at least 80% identical to the nucleic acid sequences of reported herein. More preferred phosphoglucomutase nucleic acid fragments are at least 90% identical to the sequences herein. Most preferred are phosphoglucomutase nucleic acid fragments that are at least 95% identical to the nucleic acid fragments reported herein.

Additionally the present strain is recognized as having a gene encoding an glucose-6-phosphate isomerase having about 64% identity at the amino acid level over length of 592 amino acids using a Smith-Waterman alignment algorithm (W. R. Pearson, supra) to the sequence set forth in SEQ ID NO:14. More preferred amino acid fragments are at least about 80%-90% identical to the sequences herein. Most preferred are nucleic acid fragments that are at least 95% identical to the amino acid fragments reported herein. Similarly, preferred glucose-6-phosphate isomerase encoding nucleic acid sequences corresponding to the instant seqeunces are those encoding active proteins and which are at least 80% identical to the nucleic acid sequences of reported herein. More preferred glucose-6-phosphate isomerase nucleic acid fragments are at least 90% identical to the sequences herein. Most preferred are glucose-6-phosphate isomerase nucleic acid fragments that are at least 95% identical to the nucleic acid fragments reported herein.

Additionally the present strain is recognized as having a gene encoding an phosphofructokinase having about 63% identity at the amino acid level over length of 437 amino acids using a Smith-Waterman alignment algorithm (W. R. Pearson, supra) to the sequence set forth in SEQ ID NO:16. More preferred amino acid fragments are at least about 80%-90% identical to the sequences herein. Most preferred are nucleic acid fragments that are at least 95% identical to the amino acid fragments reported herein. Similarly, preferred phosphofructokinase encoding nucleic acid sequences corresponding to the instant seqeunces are those encoding active proteins and which are at least 80% identical to the nucleic acid sequences of reported herein. More preferred phosphofructokinase nucleic acid fragments are at least 90% identical to the sequences herein. Most preferred are phosphofructokinase nucleic acid fragments that are at least 95% identical to the nucleic acid fragments reported herein.

Additionally the present strain is recognized as having a gene encoding an 6-phosphogluconate dehydratase having about 60% identity at the amino acid level over length of 618 amino acids using a Smith-Waterman alignment algorithm (W. R. Pearson, supra) to the sequence set forth in SEQ ID NO:18. More preferred amino acid fragments are at least about 80%-90% identical to the sequences herein. Most preferred are nucleic acid fragments that are at least 95% identical to the amino acid fragments reported herein. Similarly, preferred 6-phosphogluconate dehydratase encoding nucleic acid sequences corresponding to the instant seqeunces are those encoding active proteins and which are at least 80% identical to the nucleic acid sequences of reported herein. More preferred 6-phosphogluconate dehydratase nucleic acid fragments are at least 90% identical to the sequences herein. Most preferred are 6-phosphogluconate dehydratase nudeic acid fragments that are at least 95% identical to the nucleic acid fragments reported herein.

Additionally the present strain is recognized as having a gene encoding an encoding a 6-phosphogluconate-6-phosphate-1-dehydrogenase having about 58% identity at the amino acid level over length of 501 amino acids using a Smith-Waterman alignment algorithm (W. R. Pearson, supra) to the sequence set forth in SEQ ID NO:20. More preferred amino acid fragments are at least about 80%-90% identical to the sequences herein. Most preferred are nucleic acid fragments that are at least 95% identical to the amino acid fragments reported herein. Similarly, preferred 6-phosphogluconate-6-phosphate-1-dehydrogenase encoding nucleic acid sequences corresponding to the instant seqeunces are those encoding active proteins and which are at least 80% identical to the nucleic acid sequences of reported herein. More preferred 6-phosphogluconate-6-phosphate-1-dehydrogenase nucleic acid fragments are at least 90% identical to the sequences herein. Most preferred are 6-phosphogluconate-6-phosphate-1-dehydrogenase nucleic acid fragments that are at least 95% identical to the nucleic acid fragments reported herein.

Isolation of Homologs

The nucleic acid fragments of the instant invention may be used to isolate genes encoding homologous proteins from the same or other microbial species. Isolation of homologous genes using sequence-dependent protocols is well known in the art. Examples of sequence-dependent protocols include, but are not limited to, methods of nucleic acid hybridization, and methods of DNA and RNA amplification as exemplified by various uses of nucleic acid amplification technologies (e.g. polymerase chain reaction (PCR), Mullis et al., U.S. Pat. No. 4,683,202), ligase chain reaction (LCR), Tabor, S. et al., Proc. Acad. Sci. USA 82, 1074, (1985)) or strand displacement amplification (SDA, Walker, et al., Proc. Natl. Acad. Sci. U.S.A., 89, 392, (1992)).

For example, genes encoding similar proteins or polypetides to those of the instant invention could be isolated directly by using all or a portion of the instant nucleic acid fragments as DNA hybridization probes to screen libraries from any desired bacteria using methodology well known to those skilled in the art. Specific oligonucleotide probes based upon the instant nucleic acid sequences can be designed and synthesized by methods known in the art (Maniatis). Moreover, the entire sequences can be used directly to synthesize DNA probes by methods known to the skilled artisan such as random primers DNA labeling, nick translation, or end-labeling techniques, or RNA probes using available in vitro transcription systems. In addition, specific primers can be designed and used to amplify a part of or full-length of the instant sequences. The resulting amplification products can be labeled directly during amplification reactions or labeled after amplification reactions, and used as probes to isolate full length DNA fragments under conditions of appropriate stringency.

Typically, in PCR-type amplification techniques, the primers have different sequences and are not complementary to each other. Depending on the desired test conditions, the sequences of the primers should be designed to provide for both efficient and faithful replication of the target nucleic acid. Methods of PCR primer design are common and well known in the art (Thein and Wallace, “The use of oligonucleotide as specific hybridization probes in the Diagnosis of Genetic Disorders”, in Human Genetic Diseases: A Practical Approach, K. E. Davis Ed., (1986) pp. 33-50 IRL Press, Herndon, Va.; Rychlik, W. (1993) In White, B. A. (ed.), Methods in Molecular Biology, Vol. 15, pages 31-39, PCR Protocols: Current Methods and Applications. Humania Press, Inc., Totowa, N.J.).

Generally two short segments of the instant sequences may be used in polymerase chain reaction protocols to amplify longer nucleic acid fragments encoding homologous genes from DNA or RNA. The polymerase chain reaction may also be performed on a library of cloned nucleic acid fragments wherein the sequence of one primer is derived from the instant nucleic acid fragments, and the sequence of the other primer takes advantage of the presence of the polyadenylic acid tracts to the 3′ end of the mRNA precursor encoding microbial genes. Alternatively, the second primer sequence may be based upon sequences derived from the cloning vector. For example, the skilled artisan can follow the RACE protocol (Frohman et al., PNAS USA 85:8998 (1988)) to generate cDNAs by using PCR to amplify copies of the region between a single point in the transcript and the 3′ or 5′ end. Primers oriented in the 3′ and 5′ directions can be designed from the instant sequences. Using commercially available 3′ RACE or 5′ RACE systems (BRL), specific 3′ or 5′ cDNA fragments can be isolated (Ohara et al., PNAS USA 86:5673 (1989); Loh et al., Science 243:217 (1989)).

Alternatively the instant sequences may be employed as hybridization reagents for.the identification of homologs. The basic components of a nucleic acid hybridization test include a probe, a sample suspected of containing the gene or gene fragment of interest, and a specific hybridization method. Probes of the present invention are typically single stranded nucleic acid sequences which are complementary to the nucleic acid sequences to be detected. Probes are “hybridizable” to the nucleic acid sequence to be detected. The probe length can vary from 5 bases to tens of thousands of bases, and will depend upon the specific test to be done. Typically a probe length of about 15 bases to about 30 bases is suitable. Only part of the probe molecule need be complementary to the nucleic acid sequence to be detected. In addition, the complementarity between the probe and the target sequence need not be perfect. Hybridization does occur between imperfectly complementary molecules with the result that a certain fraction of the bases in the hybridized region are not paired with the proper complementary base.

Hybridization methods are well defined. Typically the probe and sample must be mixed under conditions which will permit nucleic acid hybridization. This involves contacting the probe and sample in the presence of an inorganic or organic salt under the proper concentration and temperature conditions. The probe and sample nucleic acids must be in contact for a long enough time that any possible hybridization between the probe and sample nucleic acid may occur. The concentration of probe or target in the mixture will determine the time necessary for hybridization to occur. The higher the probe or target concentration the shorter the hybridization incubation time needed. Optionally a chaotropic agent may be added. The chaotropic agent stabilizes nucleic acids by inhibiting nuclease activity. Furthermore, the chaotropic agent allows sensitive and stringent hybridization of short oligonucleotide probes at room temperature [Van Ness and Chen (1991) Nucl. Acids Res. 19:5143-5151]. Suitable chaotropic agents include guanidinium chloride, guanidinium thiocyanate, sodium thiocyanate, lithium tetrachloroacetate, sodium perchlorate, rubidium tetrachloroacetate, potassium iodide, and cesium trifluoroacetate, among others. Typically, the chaotropic agent will be present at a final concentration of about 3M. If desired, one can add formamide to the hybridization mixture, typically 30-50% (v/v).

Various hybridization solutions can be employed. Typically, these comprise from about 20 to 60% volume, preferably 30%, of a polar organic solvent. A common hybridization solution employs about 30-50% v/v formamide, about 0.15 to 1M sodium chloride, about 0.05 to 0.1M buffers, such as sodium citrate, Tris-HCl, PIPES or HEPES (pH range about 6-9), about 0.05 to 0.2% detergent, such as sodium dodecylsulfate, or between 0.5-20 mM EDTA, FICOLL (Pharmacia Inc.) (about 300-500 kilodaltons), polyvinylpyrrolidone (about 250-500 kdal), and serum albumin. Also included in the typical hybridization solution will be unlabeled carrier nucleic acids from about 0.1 to 5 mg/mL, fragmented nucleic DNA, e.g., calf thymus or salmon sperm DNA, or yeast RNA, and optionally from about 0.5 to 2% wt./vol. glycine. Other additives may also be included, such as volume exclusion agents which include a variety of polar water-soluble or swellable agents, such as polyethylene glycol, anionic polymers such as polyacrylate or polymethylacrylate, and anionic saccharidic polymers, such as dextran sulfate.

Nucleic acid hybridization is adaptable to a variety of assay formats. One of the most suitable is the sandwich assay format. The sandwich assay is particularly adaptable to hybridization under non-denaturing conditions. A primary component of a sandwich-type assay is a solid support. The solid support has adsorbed to it or covalently coupled to it immobilized nucleic acid probe that is unlabeled and complementary to one portion of the sequence.

Recombinant Expression—Microbial

The genes and gene products of the instant sequences may be produced in heterologous host cells, particularly in the cells of microbial hosts. Expression in recombinant microbial hosts may be useful for the expression of various pathway intermediates, for the modulation of pathways already existing in the host, and for the synthesis of new products heretofore not possible using the host. Additionally, the gene products may be useful for conferring higher growth yields of the host or for enabling alternative growth modes to be utilized.

Preferred heterologous host cells for expression of the instant genes and nucleic acid molecules are microbial hosts that can be found broadly within microbial families and which grow over a wide range of temperatures, pH values, and solvent tolerances. Such microbes will include generally bacteria, yeast, and filamentous fungi. Specifically, suitable yeasts and fungi will include, but are not limited to, Aspergillus, Saccharomyces, Pichia, Candida, and Hansenula. Suitable bacterial species include, but are not limited to, Salmonella, Bacillus, Acinetobacter, Rhodococcus, Streptomyces, Escherichia, and Pseudomonas. Most preferred hosts for the expression of the present carbon flux genes are members of the methanotrophic class of bacteria including Methylomonas, Methylococcus and Methylobacter. Particularly suited for transformation will be members of the genus Methylomonas. These bacterial species have the ability to convert single carbon substrates such as methane and methanol to useful products and these genes are particularly suited for substrates found in these hosts.

Of particular interest in the present invention are high growth obligate methanotrophs having an energetically favorable carbon flux pathway. For example, Applicants have discovered a specific strain of methanotroph having several pathway features which make it particularly useful for carbon flux manipulation. This type of strain has served as the host in the present application and is known as Methylomonas 16a (ATCC PTA 2402).

The present strain contains several anomalies in the carbon utilization pathway. For example, based on genome sequence data, the strain is shown to contain genes for two pathways of hexose metabolism. The Entner-Douderoff pathway which utilizes the keto-deoxy phosphogluconate aldolase enzyme is present in the strain. It is generally well accepted that this is the operative pathway in obligate methanotrophs. Also present, however, is the Embden-Meyerhof pathway which utilizes the fructose bisphosphate aldolase enzyme. It is well known that this pathway is either not present or not operative in obligate methanotrophs. Energetically, the latter pathway is most favorable and allows greater yield of biologically useful energy and ultimately production of cell mass and other cell mass-dependent products in Methylomonas 16a. The activity of this pathway in the present 16a strain has been confirmed through microarray data and biochemical evidence measuring the reduction of ATP. Although the 16a strain has been shown to possess both the Embden-Meyerhof and the Entner-Douderoff pathway enzymes, the data suggests that the Embden-Meyerhof pathway enzymes are more strongly expressed than the Entner-Douderoff pathway enzymes. This result is surprising and counter to existing beliefs concerning the glycolytic metabolism of methanotrophic bacteria. Applicants have discovered other methanotrophic bacteria having this characteristic, including for example, Methylomonas clara and Methylosinus sporium. It is likely that this activity has remained undiscovered in methanotrophs due to the lack of activity of the enzyme with ATP, the typical phosphoryl donor for the enzyme in most bacterial systems.

A particularly novel and useful feature of the Embden-Meyerhof pathway in strain 16a is that the key phosphofructokinase step is pyrophosphate dependent instead of ATP dependent. This feature adds to the energy yield of the pathway by using pyrophosphate instead of ATP. Because of its significance in providing an energetic advantage to the strain this gene in the carbon flux pathway is considered diagnostic for the present strain.

Comparison of the pyrophosphate dependent phosphofructokinase gene sequence (SEQ ID NO: 15) and deduced amino acid sequence (SEQ ID NO:16) to public databases reveals that the most similar known sequences are about 63% identical to the amino acid sequence reported herein over a length of 437 amino acids using a Smith-Waterman alignment algorithm (W. R. Pearson, Comput. Methods Genome Res., [Proc. Int. Symp.] (1994), Meeting Date 1992, 111-20. Editor(s): Suhai, Sandor. Publisher Plenum, New York, N.Y.). More preferred amino acid fragments are at least about 80%-90% identical to the sequences herein. Most preferred are nucleic acid fragments that are at least 95% identical to the amino acid fragments reported herein. Similarly, preferred pyrophosphate dependent phosphofructokinase encoding nucleic acid sequences corresponding to the instant gene are those encoding active proteins and which are at least 80% identical to the nucleic acid sequences of reported herein. More preferred pyrophosphate dependent phosphofructokinase nudeic acid fragments are at least 90% identical to the sequences herein. Most preferred are pyrophosphate dependent phosphofructokinase nucleic acid fragments that are at least 95% identical to the nucleic acid fragments reported herein.

In methanotrophic bacteria methane is converted to biomolecules via a cyclic set of reactions known as the ribulose monophosphate pathway or RuMP cycle. This pathway is comprised of three phases, each phase being a series of enzymatic steps (FIG. 1). The first step is “fixation” or incorporation of C-1 (formaldehyde) into a pentose to form a hexose or six-carbon sugar. This occurs via a condensation reaction between a 5-carbon sugar (pentose) and formaldehyde and is catalyzed by hexulose monophosphate synthase. The second phase is termed “cleavage” and results in splitting of that hexose into two 3-carbon molecules. One of those three-carbon molecules is recycled back through the RuMP pathway and the other 3-carbon fragment is utilized for cell growth. In methanotrophs and methylotrophs the RuMP pathway may occur as one of three variants. However, only two of these variants are commonly found: the FBP/TA (fructose bisphosphotaseftransaldolase) or the KDPG/TA (keto deoxy phosphogluconate/transaldolase) pathway (Dijkhuizen L., G. E. Devries. The Physiology and biochemistry of aerobic methanol-utilizing gram negative and gram positive bacteria. In: Methane and Methanol Utilizers 1992, ed Colin Murrell and Howard Dalton Plenum Press NY).

The present strain is unique in the way it handles the “cleavage” steps where genes were found that carry out this conversion via fructose bisphosphate as a key intermediate. The genes for fructose bisphosphate aldolase and transaldolase were found clustered together on one piece of DNA. Secondly, the genes for the other variant involving the keto deoxy phosphogluconate intermediate were also found clustered together. Available literature teaches that these organisms (obligate methylotrophs and methanotrophs) rely solely on the KDPG pathway and that the FBP-dependent fixation pathway is utilized by facultative methylotrophs (Dijkhuizen et al., supra). Therefore the latter observation is expected whereas the former is not. The finding of the FBP genes in an obligate methane utilizing bacterium is both surprising and suggestive of utility. The FBP pathway is energetically favorable to the host microorganism due to the fact that more energy (ATP) is utilized than is utilized in the KDPG pathway. Thus organisms that utilize the FBP pathway may have an energetic advantage and growth advantage over those that utilize the KDPG pathway. This advantage may also be useful for energy-requiring production pathways in the strain. By using this pathway, a methane-utilizing bacterium may have an advantage over other methane utilizing organisms as production platforms for either single cell protein or for any other product derived from the flow of carbon through the RuMP pathway.

Accordingly the present invention provides a method for altering carbon flux in a high growth, energetically favorable Methylomonas strain which

(a) grows on a C1 carbon substrate selected from the group consisting of methane and methanol; and

(b) comprises a functional Embden-Meyerhof carbon pathway, said pathway comprising a gene encoding a pyrophosphate dependent phosphofructokinase enzyme.

Microbial expression systems and expression vectors containing regulatory sequences that direct high level expression of foreign genes are well known to those skilled in the art. Any of these could be used to construct chimeric genes for expression of the any of the present genes. These chimeric genes could then be introduced into appropriate microorganisms via transformation to provide recombinant expression of the enzymes and manipulation of the carbon pathways.

Vectors or cassettes useful for the transformation of suitable host cells are well known in the art. Typically the vector or cassette contains sequences directing transcription and translation of the relevant gene, a selectable marker, and sequences allowing autonomous replication or chromosomal integration. Suitable vectors comprise a region 5′ of the gene which harbors transcriptional initiation controls and a region 3′ of the DNA fragment which controls transcriptional termination. It is most preferred when both control regions are derived from genes homologous to the transformed host cell, although it is to be understood that such control regions need not be derived from the genes native to the specific species chosen as a production host.

Initiation control regions or promoters, which are useful to drive expression of the instant ORF's in the desired host cell are numerous and familiar to those skilled in the art. Virtually any promoter capable of driving these genes is suitable for the present invention including but not limited to CYC1, HIS3, GAL1, GAL10, ADH1, PGK, PHO5, GAPDH, ADC1, TRP1, URA3, LEU2, ENO, TPI (useful for expression in Saccharomyces); AOX1 (useful for expression in Pichia); and lac, ara, tet, trp, IP_(L), IP_(R), T7, tac, and trc (useful for expression in Escherichia coli) as well as the amy, apr, npr promoters and various phage promoters useful for expression in Bacillus.

Termination control regions may also be derived from various genes native to the preferred hosts. Optionally, a termination site may be unnecessary, however, it is most preferred if included.

Pathway Engineering

The present genes may be used to affect carbon flow in bacteria and specifically methanotrophic bacteria. Commercial applications of the methanotrops have revolved around the production of single cell protein (Villadsen, John, Recent Trends Chem. React. Eng., [Proc. Int. Chem. React. Eng. Conf.], 2nd (1987), Volume 2, 320-33. Editor(s): Kulkarni, B. D.; Mashelkar, R. A.; Sharma, M. M. Publisher: Wiley East, New Delhi, India; Naguib, M.,Proc. OAPEC Symp. Petroprotein, [Pap.] (1980), Meeting Date 1979, 253-77, Publisher Organ. Arab Pet. Exporting Countries, Kuwait, Kuwait) and the epoxidation of alkenes for production of chemicals (U.S. Pat. No. 4,348,476). These C1 substrate utilizing bacteria also are known to produce polysaccharides, used as thickeners in food and non-food industries, and isoprenoid compounds and carotenoid pigments of various carbon lengths (Urakami et al., J. Gen. Appl. Microbiol. (1986), 32(4), 317-41). The production of all of these commercially useful products will be impacted by alterations in carbon flux, in general, and by manipulation of the present genes, in particular. Such manipulation may be effected by the up- or down-regulation of various members of the carbon flux pathway.

Many of the key genes in the carbon utilization pathway are now disclosed in the present invention. Referring to FIG. 1, for example, the present invention provides genes encoding two distinct carbon flux pathways isolated from a methanotrophic bacteria. The genes and gene products are set forth in SEQ ID NO:1-SEQ ID NO:20, and encode both a KDPG aldolase and a FBP aldolase as well as a phosphoglucomutase, pyrophosphate dependent phosphofructokinase pyrophosphate, 6-phosphogluconate dehydratase, and a glucose 6 phosphate 1 dehydrogenase. The phosphoglucomutase is responsible for the interconversion of glucose-6-phosphate to glucose-1-phosphate, which feeds into either the Entner douderoff or Embden-Meyerhof carbon flux pathways. As shown in FIG. 1, fructose-6-phosphate may be converted to either glucose-6-phosphase by glucose phophate isomerase (Entner-Douderoff) or to fructose-1,6-bisphosphate (FBP) by a phosphofructokinase (Embden-Meyerhof). Following the Embden-Meyerhof pathway, FBP is then taken to two three-carbon moieties, dihydroxyacetone and 3-phosphoglyceraldehyde by the FBP aldolase. Returning to the Entner-Douderoff pathway, glucose-6-phosphate is taken to 6phosphogluconate by a glucose-6-phosphate dehydrogenase which is subsequently taken to 2-keto-3-deoxy-6-phosphogluconate (KDPG) by a 6 phosphogluconate dehydratase. The KDPG is then converted to two three-carbon moieties (pyruvate and 3-phosphoglyceraldehyde) by a KDPG aldolase. Thus, the Embden-Meyerhof and Entner-Douderoff pathways are rejoined at the level of 3-phosphoglyceraldehyde. Manipulations in any one or all of these genes may be used for commercial advantage in the production of materials from a variety of bacteria and most suitably from methanotrophic bacteria.

Methods of manipulating genetic pathways are common and well known in the art. Selected genes in a particularly pathway may be upregulated or down regulated by variety of methods. Additionally, competing pathways in the organism may be eliminated or sublimated by gene disruption and similar techniques.

Once a key genetic pathway has been identified and sequenced, specific genes may be upregulated to increase the output of the pathway. For example, additionally copies of the targeted genes may be introduced into the host cell on multicopy plasmids such as pBR322. Alternatively the target genes may be modified so as to be under the control of non-native promoters. Where it is desired that a pathway operate at a particular point in a cell cycle or during a fermentation run, regulated or inducible promoters may used to replace the native promoter of the target gene. Similarly, in some cases the native or endogenous promoter may be modified to increase gene expression. For example, endogenous promoters can be altered in vivo by mutation, deletion, and/or substitution (see, Kmiec, U.S. Pat. No. 5,565,350; Zarling et al., PCT/US93/03868).

Alternatively it may be necessary to reduce or eliminate the expression of certain genes in the target pathway or in competing pathways that may serve as competing sinks for energy or carbon. Methods of down-regulating genes for this purpose have been explored. Where sequence of the gene to be disrupted is known, one of the most effective methods gene down regulation is targeted gene disruption where foreign DNA is inserted into a structural gene so as to disrupt transcription. This can be effected by the creation of genetic cassettes comprising the DNA to be inserted (often a genetic marker) flanked by sequence having a high degree of homology to a portion of the gene to be disrupted. Introduction of the cassette into the host cell results in insertion of the foreign DNA into the structural gene via the native DNA replication mechanisms of the cell. (See for example Hamilton et al. (1989) J. Bacteriol. 171:4617-4622, Balbas et al. (1993) Gene 136:211-213, Gueldener et al. (1996) Nucleic Acids Res. 24:2519-2524, and Smith et al. (1996) Methods Mol. Cell. Biol. 5:270-277.)

Antisense technology is another method of down regulating genes where the sequence of the target gene is known. To accomplish this, a nucleic acid segment from the desired gene is cloned and operably linked to a promoter such that the anti-sense strand of RNA will be transcribed. This construct is then introduced into the host cell and the antisense strand of RNA is produced. Antisense RNA inhibits gene expression by preventing the accumulation of mRNA which encodes the protein of interest. The person skilled in the art will know that special considerations are associated with the use of antisense technologies in order to reduce expression of particular genes. For example, the proper level of expression of antsense genes may require the use of different chimeric genes utilizing different regulatory elements known to the skilled artisan.

Although targeted gene disruption and antisense technology offer effective means of down regulating genes where the sequence is known, other less specific methodologies have been developed that are not sequence based. For example, cells may be exposed to a UV radiation and then screened for the desired phenotype. Mutagenesis with chemical agents is also effective for generating mutants and commonly used substances include chemicals that affect nonreplicating DNA such as HNO₂ and NH₂OH, as well as agents that affect replicating DNA such as acridine dyes, notable for causing frameshift mutations. Specific methods for creating mutants using radiation or chemical agents are well documented in the art. See for example Thomas D. Brock in Biotechnology: A Textbook of Industrial Microbiology, Second Edition (1989) Sinauer Associates, Inc., Sunderland, Mass., or Deshpande, Mukund V., Appl. Biochem. Biotechnol., 36, 227, (1992).

Another non-specific method of gene disruption is the use of transposoable elements or transposons. Transposons are genetic elements that insert randomly in DNA but can be latter retrieved on the basis of sequence to determine where the insertion has occurred. Both in vivo and in vftro transposition methods are known. Both methods involve the use of a transposable element in combination with a transposase enzyme. When the transposable element or transposon, is contacted with a nucleic acid fragment in the presence of the transposase, the transposable element will randomly insert into the nucleic acid fragment. The technique is useful for random mutageneis and for gene isolation, since the disrupted gene may be identified on the basis of the sequence of the transposable element. Kits for in vitro transposition are commercially available (see for example The Primer Island Transposition Kit, available from Perkin Elmer Applied Biosystems, Branchburg, N.J., based upon the yeast Ty1 element; The Genome Priming System, available from New England Biolabs, Beverly, Mass.; based upon the bacterial transposon Tn7; and the EZ::TN Transposon Insertion Systems, available from Epicentre Technologies, Madison, Wis., based upon the Tn5 bacterial transposable element.

Within the context of the present invention it may be useful to modulate the expression of the carbon flux pathway. It is apparent from the known pathways in methanotrophic bacteria that there can be utility in either the FBP/TA or KDGP/TA pathway, depending on the target product. The FBP/TA pathway is more energy-yielding and thus is advantageous from the standpoint of producing more cellular mass per unit of methane metabolized. Thus if the strain is forced to utilize this pathway via a gene knock-out of the KDGP/TA pathway, it is anticipated that greater cell mass will be produced. In addition, the production of chemicals that have a high energy requirement for biosynthesis in the form of ATP may also be enhanced by deletion or mutation of the KDGP/TA pathway. Chemical production requiring pyruvate as a key intermediate, however, might benefit from the deletion or knock-out of the FBP/TA pathway genes. As an integral part of the Methylomonas production platform it is desirable to have the capability to utilize either pathway via introduction of specialized regulatory gene promoters that will enable either pathway to be switched on or off in the presence of chemicals that could be added to the fermentation.

More specifically, it has been noted that the present Methylomonas 16a comprises genes encoding both the Entner-Douderoff and Embden-Meyerhof carbon flux pathways. Because the Embden-Meyerhof pathway is more energy efficient it may be desirable to over-express the genes in this pathway. Additionally, it is likely that the Entner-Douderoff pathway is a competitive pathway and inhibition of this pathway may lead to increased energy efficiency in the Embden-Meyerhof system. This might be accomplished by selectively using the above described methods of gene down regulation on the sequence encoding the keto-deoxy phosphogluconate aldolase (SEQ ID NO: 9) or any of the other members of the Entner-Ddouderoff system and upregulating the gene encoding the fructose bisphosphatase aldolase of the Embden-Meyerhof system (SEQ ID NO:5 OR 7). In this fashion, the carbon flux in the present Methylomonas 16a may be optimized. Additionally, where the present strain has been engineered to produce specific organic materials such as aromatics for monomer production, optimization of the carbon flux pathway will lead to increased yields of these materials.

Industrial Scale Production

Where the engineering of a commercial bacterial production plafform comprising the present genes is desired, a variety of culture methodologies may be applied. For example, large scale production of a specific product or products from a recombinant microbial host may be produced by both batch or continuous culture methodologies

A classical batch culturing method is a closed system where the composition of the media is set at the beginning of the culture and not subject to artificial alterations during the culturing process. Thus, at the beginning of the culturing process the media is inoculated with the desired organism or organisms and growth or metabolic activity is permitted to occur adding nothing to the system. Typically, however, a “batch” culture is batch with respect to the addition of carbon source and attempts are often made at controlling factors such as pH and oxygen concentration. In batch systems the metabolite and biomass compositions of the system change constantly up to the time the culture is terminated. Within batch cultures cells moderate through a static lag phase to a high growth log phase and finally to a stationary phase where growth rate is diminished or halted. If untreated, cells in the stationary phase will eventually die. Cells in log phase are often responsible for the bulk of production of end product or intermediate in some systems. Stationary or post xponential phase production can be obtained in other systems.

A variation on the standard batch system is the Fed-Batch system. Fed-Batch culture processes are also suitable in the present invention and comprise a typical batch system with the exception that the substrate is added in increments as the culture progresses. Fed-Batch systems are useful when catabolite repression is apt to inhibit the metabolism of the cells and where it is desirable to have limited amounts of substrate in the media. Measurement of the actual substrate concentration in Fed-Batch systems is difficult and is therefore estimated on the basis of the changes of measurable factors such as pH, dissolved oxygen and the partial pressure of waste gases such as CO₂. Batch and Fed-Batch culturing methods are common and well known in the art and examples may be found in Thomas D. Brock in Biotechnology: A Textbook of Industrial Microbiology, Second Edition (1989) Sinauer Associates, Inc., Sunderland, Mass., or Deshpande, Mukund V., Appl. Biochem. Biotechnol., 36, 227, (1992), herein incorporated by reference.

Commercial use of the instant gene pathways may also be accomplished with a continuous culture. Continuous cultures are an open system where a defined culture media is added continuously to a bioreactor and an equal amount of conditioned media is removed simultaneously for processing. Continuous cultures generally maintain the cells at a constant high liquid phase density where cells are primarily in log phase growth. Alternatively continuous culture may be practiced with immobilized cells where carbon and nutrients are continuously added and valuable products, by-products or waste products continuously removed from the cell mass. Cell immobilization may be performed using a wide range of solid supports composed of natural and/or synthetic materials.

Continuous or semi-continuous culture allows for the modulation of one factor or any number of factors that affect cell growth or end product concentration. For example, one method will maintain a limiting nutrient such as the carbon source or nitrogen level at a fixed rate and allow all other parameters to moderate. In other systems a number of factors affecting growth can be altered continuously while the cell concentration, measured by media turbidity, is kept constant. Continuous systems strive to maintain steady state growth conditions and thus the cell loss due to media being drawn off must be balanced against the cell growth rate in the culture. Methods of modulating nutrients and growth factors for continuous culture processes as well as techniques for maximizing the rate of product formation are well known in the art of industrial microbiology and a variety of methods are detailed by Brock, supra.

Protein Engineering

It is contemplated that the present nucleotide sequences may be used to produce gene products having enhanced or altered activity. Various methods are known for mutating a native gene sequence to produce a gene product with altered or enhanced activity including but not limited to error prone PCR (Melnikov et al., Nucleic Acids Research, (Feb. 15, 1999) Vol. 27, No. 4, pp. 1056-1062); site directed mutagenesis (Coombs et al., Proteins (1998), 259-311, 1 plate. Editor(s): Angeletti, Ruth Hogue. Publisher: Academic, San Diego, Calif.) and “gene shuffling” (U.S. Pat. No. 5,605,793; U.S. Pat. No. 5,811,238; U.S. Pat. No. 5,830,721; and U.S. Pat. No. 5,837,458, incorporated herein by reference).

The method of gene shuffling is particularly attractive due to its facile implementation, and high rate of mutagenesis and ease of screening. The process of gene shuffling involves the restriction endonuclease cleavage of a gene of interest into fragments of specific size in the presence of additional populations of DNA regions of both similarity to or difference to the gene of interest. This pool of fragments will then be denatured and reannealed to create a mutated gene. The mutated gene is then screened for altered activity.

The carbon flux sequences of the present invention may be mutated and screened for altered or enhanced activity by this method. The sequences should be double stranded and can be of various lengths ranging form 50 bp to 10 kb. The sequences may be randomly digested into fragments ranging from about 10 bp to 1000 bp, using restriction endonucleases well known in the art (Maniatis supra). In addition to the instant microbial sequences, populations of fragments that are hybridizable to all or portions of the microbial sequence may be added. Similarly, a population of fragments which are not hybridizable to the instant sequence may also be added. Typically these additional fragment populations are added in about a 10 to 20 fold excess by weight as compared to the total nucleic acid. Generally if this process is followed the number of different specific nucleic acid fragments in the mixture will be about 100 to about 1000. The mixed population of random nucleic acid fragments are denatured to form single-stranded nucleic acid fragments and then reannealed. Only those single-stranded nucleic acid fragments having regions of homology with other single-stranded nucleic acid fragments will reanneal. The random nucleic acid fragments may be denatured by heating. One skilled in the art could determine the conditions necessary to completely denature the double stranded nucleic acid. Preferably the temperature is from 80° C. to 100° C. The nucleic acid fragments may be reannealed by cooling. Preferably the temperature is from 20° C. to 75° C. Renaturation can be accelerated by the addition of polyethylene glycol (“PEG”) or salt. A suitable salt concentration may range from 0 mM to 200 mM. The annealed nucleic acid fragments are next incubated in the presence of a nucleic acid polymerase and dNTP's (i.e. dATP, dCTP, dGTP and dTTP). The nucleic acid-polymerase may be the Klenow fragment, the Taq polymerase or any other DNA polymerase known in the art. The polymerase may be added to the random nudeic acid fragments prior to annealing, simultaneously with annealing or after annealing. The cycle of denaturation, renaturation and incubation in the presence of polymerase is repeated for a desired number of times. Preferably the cycle is repeated from 2 to 50 times, more preferably the sequence is repeated from 10 to 40 times. The resulting nucleic acid is a larger double-stranded polynucleotide of from about 50 bp to about 100 kb and may be screened for expression and altered activity by standard cloning and expression protocol. (Maniatis supra).

Gene Expression Profiling

The present carbon flux genes may be used in connection with gene expression profiling technology for metabolic characterization of the cell from which the genes came. For example, many external changes such as changes in growth condition or exposure to chemicals can cause induction or repression of genes in the cell. The induction or repression of genes can be used for a screening system to determine the best growth conditions for a production organism and drug discovery with similar mode of action compound, just to mention a few. On the other hand, by amplifying or disrupting genes, one can manipulate the production of the amount of cellular products as well as the timeline upon which those products are produced. All or a portion of the present nucleic acid fragments of the instant invention may be used as probes for gene expression monitoring and gene expression profiling.

For example, all or a portion of the instant nucleic acid fragments may be immobilized on a nylon membrane or a glass slide. A Generation II DNA spotter (Molecular Dynamics) is one of the available technologies to array the DNA samples onto the coated glass slides. Other array methods are also available and well known in the art. After the cells are grown in various growth conditions or treated with potential candidates, cellular RNA is purified. Fluorescent or radioactive labeled target cDNA can be made by reverse transcription of mRNA. The target mixture is hybridized to the probes and washed using conditions well known in the art. The amount of the target gene expression is quantified by the intensity of radioactivity or fluorescence labels (e.g., confocal laser microscope: Molecular Dynamics). The intensities of radioactivity or fluorescent label at the immobilized probes are measured using technology well known in the art. The two color fluorescence detection scheme (e.g., Cy3 and Cy5) has the advantage over radioactively labeled targets by allowing rapid and simultaneous differential expression analysis of independent samples. In addition, the use of ratio measurements compensates for probe to probe variation of intensity due to DNA concentration and hybridization efficiency. In the case of fluorescence labeling, the two fluorescent images obtained with the appropriate excitation and emission filters constitute the raw data from which differential gene expression ratio values are calculated. The intensity of images are analyzed using the available software (e.g., Array Vision 4.0: Imaging Research Inc.) well known in the art and normalized to compensate for the differential efficiencies of labeling and detection of the label. There are many different ways known in the art to normalize the signals. One of the ways to normalize the signal is by correcting the signal against internal controls. Another way is to run a separate array with labeled genomic driven DNA and compare the signal with mRNA driven signals. This method also allows measurement of the transcript abundance. The array data of individual genes is examined and evaluated to determine the induction or repression of each gene under the test conditions.

EXAMPLES

The present invention is further defined in the following Examples. It should be understood that these Examples, while indicating preferred embodiments of the invention, are given by way of illustration only. From the above discussion and these Examples, one skilled in the art can ascertain the essential characteristics of this invention, and without departing from the spirit and scope thereof, can make various changes and modifications of the invention to adapt it to various usages and conditions.

General Methods

Standard recombinant DNA and molecular cloning techniques used in the Examples are well known in the art and are described by Sambrook, J., Fritsch, E. F. and Maniatis, T. Molecular Cloning: A Laboratory Manual; Cold Spring Harbor Laboratory Press: Cold Spring Harbor, (1989) (Maniatis) and by T. J. Silhavy, M. L. Bennan, and L. W. Enquist, Experiments with Gene Fusions, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. (1984) and by Ausubel, F. M. et al., Current Protocols in Molecular Biology, pub. by Greene Publishing Assoc. and Wiley-lnterscience (1987).

Materials and methods suitable for the maintenance and growth of bacterial cultures are well known in the art. Techniques suitable for use in the following examples may be found as set out in Manual of Methods for General Bacteriology (Phillipp Gerhardt, R. G. E. Murray, Ralph N. Costilow, Eugene W. Nester, Willis A. Wood, Noel R. Krieg and G. Briggs Phillips, eds), American Society for Microbiology, Washington, D.C. (1994)) or by Thomas D. Brock in Biotechnology: A Textbook of Industrial Microbiology, Second Edition, Sinauer Associates, Inc., Sunderland, Mass. (1989), All reagents, restriction enzymes and materials used for the growth and maintenance of bacterial cells were obtained from Aldrich Chemicals (Milwaukee, Wis.), DIFCO Laboratories (Detroit, Mich.), GIBCO/BRL (Gaithersburg, Md.), or Sigma Chemical Company (St. Louis, Mo.) unless otherwise specified.

Manipulations of genetic sequences were accomplished using the suite of programs available from the Genetics Computer Group Inc. (Wisconsin Package Version 9.0, Genetics Computer Group (GCG), Madison, Wis.). Where the GCG program “Pileup” was used the gap creation default value of 12, and the gap extension default value of 4 were used. Where the CGC “Gap” or “Besffit” programs were used the default gap creation penalty of 50 and the default gap extension penalty of 3 were used. In any cases where GCG program parameters were not prompted for, in these or any other GCG program, default values were used.

Multiple alignment of the sequences was performed using the FASTA program incorporating the Smith-Waterman algorithm (W. R. Pearson, Comput. Methods Genome Res., [Proc. Int. Symp.] (1994), Meeting Date 1992, 111-20. Editor(s): Suhai, Sandor. Publisher Plenum, New York, N.Y.).

The meaning of abbreviations is as follows: “h” means hour(s), “min” means minute(s), “sec” means second(s), “d” means day(s), “mL” means milliliters, “L” means liters.

Example 1 Isolation of Methylomonas 16a

The original environmental sample containing the isolate was obtained from pond sediment. The pond sediment was inoculated directly into a defined mineral medium under 25% methane in air. Methane was the sole source of carbon and energy. Growth was followed until the opticaldensity at 660 nm was stable whereupon the culture was transferred to fresh medium such that a 1:100 dilution was achieved. After 3 successive transfers with methane as sole carbon and energy source the culture was plated onto defined minimal medium agar and incubated under 25% methane in air. Many methanotrophic bacterial species were isolated in this manner. However, Methylomonas 16a was selected as the organism to study due to the rapid growth of colonies, large colony size, ability to grow on minimal media, and pink pigmentation indicative of an active biosynthetic pathway for carotenoids.

Example 2 Preparation of Genomic DNA for Sequencing and Seqeunce Generation

Genomic DNA was isolated from Methylomonas 16a according to standard protocols.

Genomic DNA and library construction were prepared according to published protocols (Fraser et al The Minimal Gene Complement of Mycoplasma genitalium; Science 270, 1995). A cell pellet was resuspended in a solution containing 100 mM Na-EDTA pH 8.0, 10 mM tris-HCl pH 8.0, 400 mM NaCl, and 50 mM MgCl2.

Genomic DNA preparation After resuspension, the cells were gently lysed in 10% SDS, and incubated for 30 minutes at 55° C. After incubation at room temperature, proteinase K was added to 100 μg/ml and incubated at 37° C. until the suspension was clear. DNA was extracted twice with tris-equilibrated phenol and twice with chloroform. DNA was precipitated in 70% ethanol and resuspended in a solution containing 10 mM tris-HCl and 1 mM Na-EDTA (TE) pH 7.5. The DNA solution was treated with a mix of RNAases, then extracted twice with trisequilibrated phenol and twice with chloroforrn. This was followed by precipitation in ethanol and resuspension in TE.

Library construction 200 to 500 μg of chromosomal DNA was resuspended in a solution of 300 mM sodium acetate, 10 mM tris-HCl, 1 mM Na-EDTA, and 30% glycerol, and sheared at 12 psi for 60 sec in an Aeromist Downdraft Nebulizer chamber (IBI Medical products, Chicago, Ill.). The DNA was precipitated, resuspended and treated with Bal31 nuclease. After size fractionation, a fraction (2.0 kb, or 5.0 kb) was excised, cleaned and a two-step ligation procedure was used to produce a high titer library with greater than 99% single inserts.

Sequencing A shotgun sequencing strategy approach was adopted for the sequencing of the whole microbial genome (Fleischmann, Robert et al Whole-Genorne Random sequencing and assembly of Haemophilus influenzae Rd Science, 269: 1995).

Sequence was generated on an ABI Automatic sequencer using dye terminator technology (U.S. Pat. No. 5,366,860; EP 272007) using a combination of vector and insert-specific primers. Sequence editing was performed in either DNAStar (DNA Star Inc.) or the Wisconsin GCG program (Wisconsin Package Version 9.0, Genetics Computer Group (GCG), Madison, Wis.) and the CONSED package (version 7.0). All sequences represent coverage at least two times in both directions.

Example 3

Identification and Characterization of Bacteria ORF's The carbon flux genes isolated from Methylomonas 16a were identified by conducting BLAST (Basic Local Alignment Search Tool; Altschul, S. F., et al., (1993) J. Mol. Biol. 215:403-410; see also www.ncbi.nlm.nih.gov/BLAST/) searches for similarity to sequences contained in the BLAST “nr” database (comprising all non-redundant GenBank CDS translations, sequences derived from the 3-dimensional structure Brookhaven Protein Data Bank, the SWISS-PROT protein sequence database, EMBL, and DDBJ databases). The sequences obtained in Example 1 were analyzed for similarity to all publicly available DNA sequences contained in the “nr” database using the BLASTN algorithm provided by the National Center for Biotechnology Information (NCBI). The DNA sequences were translated in all reading frames and compared for similarity to all publicly available protein sequences contained in the “nr” database using the BLASTX algorithm (Gish, W. and States, D. J. (1993) Nature Genetics 3:266-272) provided by the NCBI. All comparisons were done using either the BLASTNnr or BLASTXnr algorithm. The results of the BLAST comparison is given in Table 1 which summarize the sequences to which they have the most similarity. Table 1 displays data based on the BLASTXnr algorithm with values reported in expect values. The Expect value estimates the statistical significance of the match, specifying the number of matches, with a given score, that are expected in a search of a database of this size absolutely by chance.

TABLE 1 Genes Characterized From Methylomonas 16a SEQ ID % % Gene Name Similarity Identified SEQ ID Peptide Identity^(a) Similarity^(b) E-value^(c) Citation Transaldolase Transaldolase 1 2 78% 90% 2.7e-92 Kohler, U., et al., GI:1729831 Plant Mol. Biol. 30 (1), Anabaena variabilis. 213-218 (1996) MIPB - Transaldolase 3 4 50% 79% 1e-23 Blattner F. R. et. al transaldolase GI:7443254 Science 277:1453- Escherichia coli 1474 (1997). FBA or FDA Fructose 5 6 76% 92% 4.1e-111 Alefounder P. R. et. al. bisphosphate Mol. Microbiol. 3:723- aldolase 732 (1989). FBA or FDA Fructose 7 8 40% 70% 2.3e-39 van den Bergh E. R. bisphosphate et al.; J. Bacteriol. aldolase 178:888-893 (1996). KHG/KDPG (AL352972) 9 10 59% 72% 1e-64 Redenbach et al., Mol. Aldolase KHG/KDPG Microbiol. 21 (1), 77-96 aldolase (1996) Streptomyces coelicolor Phosphoglucomutase Phosphoglucomutase 11 12 65% 85% 1.7e-140 Lepek et al., Direct (Glucose Submission Phosphomutase) |gb|AAD03475.1| (Pgm)>>gi|3241933| gb|AAD03475.1| Glucose 6 Glucose 6 13 14 64% 81% 1.6e-136 Blattner et al., Nucleic phosphate phosphate Acids Res. 21 (23), isomerase isomerase 5408-5417 (1993) gi|396360|gb| AAC43119.1 Phosphofructokinase Phosphofructokinase 15 16 63% 83% 1.7e-97 Ladror et al., J. Biol. pyrophosphate pyrophosphate Chem. 266, 16550- dependent dependent 16555 (1991) gi|150931|gb| AAA25675.1| (M67447) 6-Phosphogluconate 6-Phosphogluconate 17 18 60% 85% 1.6e-141 Willis et al., J. Bacteriol. dehydratase dehydratase 181 (14), 4176-4184 gi|4210902|gb| (1999) AAD12045.1| (AF045609) Glucose 6 Glucose 6 19 20 58% 85% 9.4e-123 Hugouvieux-Cotte- phosphate 1 phosphate 1 Paltat, N, TITLE Direct dehydrogenase dehydrogenase Submission, gi|397854|emb| gi|397854|emb| CAA52858.1| CAA52858.1| (X74866) (X74866) ^(a)% Identity is defined as percentage of amino acids that are identical between the two proteins. ^(b)% Similarity is defined as percentage of amino acids that are identical or conserved between the two proteins. ^(c)Expect value. The Expect value estimates the statistical significance of the match, specifying the number of matches, with a given score, that are expected in a search of a database of this size absolutely by chance

20 1 984 DNA METHYLOMONAS SP. 1 atggcaagaa acttacttga gcaactccgc gagatgaccg ttgttgttgc cgataccggt 60 gacatccagg cgatcgaaac cttcaagccg cgcgatgcaa cgaccaaccc gtctttgatc 120 accgccgcgg cgcaaatgcc gcaatatcaa ggcatcgttg acgacacctt gaaaggtgcg 180 cgtgcgacgt tgggtgccag cgcttcggct gccgaggtgg cttcattggc gttcgatcgt 240 ttggcggttt ctttcggttt gaaaatcctg gaaatcatcg aaggtcgcgt ttccaccgag 300 gttgatgcgc gtttgtctta tgacaccgaa ggcactattg ccaaaggccg ggatctgatc 360 aaacaatacg aagctgcagg tgtttccaaa gagcgcgtac tgatcaaaat tgccgcgacc 420 tgggaaggca tccaggcggc tgccgttttg gaaaaagaag gtattcacac caacttgacc 480 ctgttgttcg gtctgcacca ggcgattgct tgtgccgaaa acggcattac cctgatttct 540 ccgtttgtcg gccgtattct ggactggtac aaaaaagaca ctggccgcga ctcttatcct 600 tccaacgaag atcctggcgt attgtctgta actgaagttt ataactacta caaaaaattt 660 ggttataaaa ctgaagtcat gggcgcgagc ttccgtaaca tcggcgaaat caccgaattg 720 gcgggttgcg atctgttgac catcgcgcct tctctgctgg ccgaactgca atccgttgaa 780 ggtgatttgc cacgcaaact ggaccctgca aaagcagccg gttcttcgat cgaaaaaatc 840 agcgttgaca aagcgacttt cgagcgcatg cacgaagaaa accgcatggc caaagaaaaa 900 ctggccgaag gtatcgacgg ttttgcgaaa gcgttggaaa ccttggaaaa attgttggcg 960 gatcgtttgg ctgctctgga agca 984 2 328 PRT METHYLOMONAS SP. 2 Met ala Arg Asn Leu Leu Glu Gln Leu Arg Glu Met Thr Val Val Val 1 5 10 15 Ala Asp Thr Gly Asp Ile Gln Ala Ile Glu Thr Phe Lys Pro Arg Asp 20 25 30 Ala Thr Thr Asn Pro Ser Leu Ile Thr Ala Ala Ala Gln Met Pro Gln 35 40 45 Tyr Gln Gly Ile Val Asp Asp Thr Leu Lys Gly Ala Arg Ala Thr Leu 50 55 60 Gly Ala Ser Ala Ser Ala Ala Glu Val Ala Ser Leu Ala Phe Asp Arg 65 70 75 80 Leu Ala Val Ser Phe Gly Leu Lys Ile Leu Glu Ile Ile Glu Gly Arg 85 90 95 Val Ser Thr Glu Val Asp Ala Arg Leu Ser Tyr Asp Thr Glu Gly Thr 100 105 110 Ile Ala Lys Gly Arg Asp Leu Ile Lys Gln Tyr Glu Ala Ala Gly Val 115 120 125 Ser Lys Glu Arg Val Leu Ile Lys Ile Ala Ala Thr Trp Glu Gly Ile 130 135 140 Gln Ala Ala Ala Val Leu Glu Lys Glu Gly Ile His Thr Asn Leu Thr 145 150 155 160 Leu Leu Phe Gly Leu His Gln Ala Ile Ala Cys Ala Glu Asn Gly Ile 165 170 175 Thr Leu Ile Ser Pro Phe Val Gly Arg Ile Leu Asp Trp Tyr Lys Lys 180 185 190 Asp Thr Gly Arg Asp Ser Tyr Pro Ser Asn Glu Asp Pro Gly Val Leu 195 200 205 Ser Val Thr Glu Val Tyr Asn Tyr Tyr Lys Lys Phe Gly Tyr Lys Thr 210 215 220 Glu Val Met Gly Ala Ser Phe Arg Asn Ile Gly Glu Ile Thr Glu Leu 225 230 235 240 Ala Gly Cys Asp Leu Leu Thr Ile Ala Pro Ser Leu Leu Ala Glu Leu 245 250 255 Gln Ser Val Glu Gly Asp Leu Pro Arg Lys Leu Asp Pro Ala Lys Ala 260 265 270 Ala Gly Ser Ser Ile Glu Lys Ile Ser Val Asp Lys Ala Thr Phe Glu 275 280 285 Arg Met His Glu Glu Asn Arg Met ala Lys Glu Lys Leu Ala Glu Gly 290 295 300 Ile Asp Gly Phe Ala Lys Ala Leu Glu Thr Leu Glu Lys Leu Leu Ala 305 310 315 320 Asp Arg Leu Ala Ala Leu Glu Ala 325 3 480 DNA METHYLOMONAS SP. 3 atggccgcgg gcggcgtggg cttgacgcaa ttgctgccag aactggccga agctattggt 60 ccgacgagcc gatttcatgt gcaggtcatt ggtgacacgg tggaggacat cgttgcggaa 120 gccaaacggc tacacgattt gcccgtcgac atagtggtga aaattccggc gcatggcgcc 180 ggactggcgg ccatcaagca gatcaagcgc cacgatattc cggtgctggc gacagcgatt 240 tacaacgtgc agcaaggttg gctggcggct ttgaacggcg ccgattatct ggcgccttat 300 ctgaatcgcg tcgataacca gggttttgac ggtattggcg tggtcgccga tctgcagagc 360 ttgatcgacc ggtatcaaat gcccaccaaa ctcctggtag cgagcttcaa aaacgtacaa 420 caggtgctgc aggtgttgaa actgggcgtg gcgtcggtga cgctgccttt ggacattgtg 480 4 160 PRT METHYLOMONAS SP. 4 Met ala Ala Gly Gly Val Gly Leu Thr Gln Leu Leu Pro Glu Leu Ala 1 5 10 15 Glu Ala Ile Gly Pro Thr Ser Arg Phe His Val Gln Val Ile Gly Asp 20 25 30 Thr Val Glu Asp Ile Val Ala Glu Ala Lys Arg Leu His Asp Leu Pro 35 40 45 Val Asp Ile Val Val Lys Ile Pro Ala His Gly Ala Gly Leu Ala Ala 50 55 60 Ile Lys Gln Ile Lys Arg His Asp Ile Pro Val Leu Ala Thr Ala Ile 65 70 75 80 Tyr Asn Val Gln Gln Gly Trp Leu Ala Ala Leu Asn Gly Ala Asp Tyr 85 90 95 Leu Ala Pro Tyr Leu Asn Arg Val Asp Asn Gln Gly Phe Asp Gly Ile 100 105 110 Gly Val Val Ala Asp Leu Gln Ser Leu Ile Asp Arg Tyr Gln Met Pro 115 120 125 Thr Lys Leu Leu Val Ala Ser Phe Lys Asn Val Gln Gln Val Leu Gln 130 135 140 Val Leu Lys Leu Gly Val Ala Ser Val Thr Leu Pro Leu Asp Ile Val 145 150 155 160 5 1005 DNA METHYLOMONAS SP. 5 atggctttag tgtcattgcg acaacttttg gattatgcgg ccgagcatgg ctttgccgtg 60 ccggcgttca acgtcagcaa catggagcag gtacaggcca tcatgcaggc ggccgctgcc 120 tgcgatagtc cagtgatcat gcaaggttcg gccggcgcca accgctatgc cggcgaagtg 180 tttctacggc atttgatatt ggcggccgtg gagcaatatc cgcatattcc ggtcgtcatg 240 caccgcgacc atgcacccac gcccgacatc tgcgcgcaag ccatacaatc gggcttcagc 300 tcggtgatga tggacggttc gttgctggca gacatgaaaa ccccggcttc ttttgcatac 360 aacgtcgacg tcacccgcac cgtggtcaag atggcgcatg cctgcggcgt atcggtggaa 420 ggcgaaatcg gctgcctggg agcgctggag gccaagtccg cgcaagatca cagccgtttg 480 ctgaccgatc ccgacgaagc ggtcgaattc gtcgaacaga cccaggtcga tgccgtggcc 540 gtggccatcg gcaccagcca cggcgcctat aaattcagca agccgcccac cggcgaagtg 600 ctggtgatca gtcgattgaa agaactgcag caacgactgc caaataccca ttttgtgatg 660 catggctcca gttcggtgcc gcaggattgg ttgaaaatca tcaacgatta tggcggcgat 720 attccggaaa cctatggcgt gccggtcgaa gaaatcgtcg aaggcataaa atatggtgtg 780 cgcaaggtca acatcgatac cgacctgcgc atggcgtcca ccggcgcgat gcgcaggttt 840 ctggcccaac cggaaaacgc ctcggagcta gacgcgcgca agacctatca agccgccagg 900 gacgcaatgc aggcattatg ccaggctcgc tacgaagcgt tcggttcggc gggacatgcc 960 ggcaaaatca aaccggtttc actggcggca atggccaaac gctat 1005 6 335 PRT METHYLOMONAS SP. 6 Met ala Leu Val Ser Leu Arg Gln Leu Leu Asp Tyr Ala Ala Glu His 1 5 10 15 Gly Phe Ala Val Pro Ala Phe Asn Val Ser Asn Met Glu Gln Val Gln 20 25 30 Ala Ile Met Gln Ala Ala Ala Ala Cys Asp Ser Pro Val Ile Met Gln 35 40 45 Gly Ser Ala Gly Ala Asn Arg Tyr Ala Gly Glu Val Phe Leu Arg His 50 55 60 Leu Ile Leu Ala Ala Val Glu Gln Tyr Pro His Ile Pro Val Val Met 65 70 75 80 His Arg Asp His Ala Pro Thr Pro Asp Ile Cys Ala Gln Ala Ile Gln 85 90 95 Ser Gly Phe Ser Ser Val Met Met Asp Gly Ser Leu Leu Ala Asp Met 100 105 110 Lys Thr Pro Ala Ser Phe Ala Tyr Asn Val Asp Val Thr Arg Thr Val 115 120 125 Val Lys Met ala His Ala Cys Gly Val Ser Val Glu Gly Glu Ile Gly 130 135 140 Cys Leu Gly Ala Leu Glu Ala Lys Ser Ala Gln Asp His Ser Arg Leu 145 150 155 160 Leu Thr Asp Pro Asp Glu Ala Val Glu Phe Val Glu Gln Thr Gln Val 165 170 175 Asp Ala Val Ala Val Ala Ile Gly Thr Ser His Gly Ala Tyr Lys Phe 180 185 190 Ser Lys Pro Pro Thr Gly Glu Val Leu Val Ile Ser Arg Leu Lys Glu 195 200 205 Leu Gln Gln Arg Leu Pro Asn Thr His Phe Val Met His Gly Ser Ser 210 215 220 Ser Val Pro Gln Asp Trp Leu Lys Ile Ile Asn Asp Tyr Gly Gly Asp 225 230 235 240 Ile Pro Glu Thr Tyr Gly Val Pro Val Glu Glu Ile Val Glu Gly Ile 245 250 255 Lys Tyr Gly Val Arg Lys Val Asn Ile Asp Thr Asp Leu Arg Met ala 260 265 270 Ser Thr Gly Ala Met Arg Arg Phe Leu Ala Gln Pro Glu Asn Ala Ser 275 280 285 Glu Leu Asp Ala Arg Lys Thr Tyr Gln Ala Ala Arg Asp Ala Met Gln 290 295 300 Ala Leu Cys Gln Ala Arg Tyr Glu Ala Phe Gly Ser Ala Gly His Ala 305 310 315 320 Gly Lys Ile Lys Pro Val Ser Leu Ala Ala Met ala Lys Arg Tyr 325 330 335 7 1074 DNA METHYLOMONAS SP. 7 atgacaaaaa tcttagatgt tgtaaaaccc ggcgttgtca ccggtgaaga tgtgcaaaaa 60 attttcgcaa tctgcaaaga aaacaacttt gccttgccag ccgtcaacgt gatcagtacc 120 gataccatta atgcggtatt ggaagcggcc gccaaagcca aatcacctgt tgttatccag 180 ttttcaaatg gcggcgcggc tttcgttgcc ggtaaaggtt tgaaattgga aggtcaaggc 240 tgttcgattc atggtgccat ttcaggtgct caccacgttc accgcttggc ggaactctat 300 ggtgtacctg tcgttctgca taccgaccac gcggcgaaaa aattgctgcc atgggtagat 360 ggtatgctgg atgaaggtga aaaattcttt gcggccaccg gcaagccttt gttcagctcg 420 cacatgctgg acttgtccga agagagcctg gaagaaaaca tcgaaatctg cggtaaatac 480 ttggcgcgca tggcgaaaat gggtatgacc ttggaaatcg aactgggctg caccggcggt 540 gaagaagacg gcgtggacaa cagcggcatg gatcattccg cgttgtacac ccagccggaa 600 gacgtggctt acgcgtatga gcacctgagc aaaatcagcc ctaacttcac gattgcggct 660 tctttcggca acgtgcacgg cgtttactcg ccaggaaacg tcaagctgac gccaaaaatt 720 ctggataact cgcaaaaata cgtatccgaa aaattcggct tgccagctaa atcattgacc 780 ttcgtattcc atggcggctc tggttcgtct ccggaagaaa tcaaggaatc catcagctat 840 ggcgtagtga aaatgaacat cgataccgat acccaatggg caacctggga aggcgtgatg 900 aacttctaca agaaaaacga aggctatctg caaggccaga tcggcaatcc ggaaggtgcc 960 gacaagccga acaaaaaata ctatgaccca cgcgtatggc aacgtgccgg ccaagaaggc 1020 atggttgcac gtctgcaaca agcattccag gaattgaatg cagtaaacac gctg 1074 8 358 PRT METHYLOMONAS SP. 8 Met Thr Lys Ile Leu Asp Val Val Lys Pro Gly Val Val Thr Gly Glu 1 5 10 15 Asp Val Gln Lys Ile Phe Ala Ile Cys Lys Glu Asn Asn Phe Ala Leu 20 25 30 Pro Ala Val Asn Val Ile Ser Thr Asp Thr Ile Asn Ala Val Leu Glu 35 40 45 Ala Ala Ala Lys Ala Lys Ser Pro Val Val Ile Gln Phe Ser Asn Gly 50 55 60 Gly Ala Ala Phe Val Ala Gly Lys Gly Leu Lys Leu Glu Gly Gln Gly 65 70 75 80 Cys Ser Ile His Gly Ala Ile Ser Gly Ala His His Val His Arg Leu 85 90 95 Ala Glu Leu Tyr Gly Val Pro Val Val Leu His Thr Asp His Ala Ala 100 105 110 Lys Lys Leu Leu Pro Trp Val Asp Gly Met Leu Asp Glu Gly Glu Lys 115 120 125 Phe Phe Ala Ala Thr Gly Lys Pro Leu Phe Ser Ser His Met Leu Asp 130 135 140 Leu Ser Glu Glu Ser Leu Glu Glu Asn Ile Glu Ile Cys Gly Lys Tyr 145 150 155 160 Leu Ala Arg Met ala Lys Met Gly Met Thr Leu Glu Ile Glu Leu Gly 165 170 175 Cys Thr Gly Gly Glu Glu Asp Gly Val Asp Asn Ser Gly Met Asp His 180 185 190 Ser Ala Leu Tyr Thr Gln Pro Glu Asp Val Ala Tyr Ala Tyr Glu His 195 200 205 Leu Ser Lys Ile Ser Pro Asn Phe Thr Ile Ala Ala Ser Phe Gly Asn 210 215 220 Val His Gly Val Tyr Ser Pro Gly Asn Val Lys Leu Thr Pro Lys Ile 225 230 235 240 Leu Asp Asn Ser Gln Lys Tyr Val Ser Glu Lys Phe Gly Leu Pro Ala 245 250 255 Lys Ser Leu Thr Phe Val Phe His Gly Gly Ser Gly Ser Ser Pro Glu 260 265 270 Glu Ile Lys Glu Ser Ile Ser Tyr Gly Val Val Lys Met Asn Ile Asp 275 280 285 Thr Asp Thr Gln Trp Ala Thr Trp Glu Gly Val Met Asn Phe Tyr Lys 290 295 300 Lys Asn Glu Gly Tyr Leu Gln Gly Gln Ile Gly Asn Pro Glu Gly Ala 305 310 315 320 Asp Lys Pro Asn Lys Lys Tyr Tyr Asp Pro Arg Val Trp Gln Arg Ala 325 330 335 Gly Gln Glu Gly Met Val Ala Arg Leu Gln Gln Ala Phe Gln Glu Leu 340 345 350 Asn Ala Val Asn Thr Leu 355 9 636 DNA METHYLOMONAS SP. 9 gaaaatacta tgtccgtcac catcaaagaa gtcatgacca cctcgcccgt tatgccggtc 60 atggtcatca atcatctgga acatgccgtc cctctggctc gcgcgctagt cgacggtggc 120 ttgaaagttt tggagatcac attgcgcacg ccggtggcac tggaatgtat ccgacgtatc 180 aaagccgaag taccggacgc catcgtcggc gcgggcacca tcatcaaccc tcataccttg 240 tatcaagcga ttgacgccgg tgcggaattc atcgtcagcc ccggcatcac cgaaaatcta 300 ctcaacgaag cgctagcatc cggcgtgcct atcctgcccg gcgtcatcac acccagcgag 360 gtcatgcgtt tattggaaaa aggcatcaat gcgatgaaat tctttccggc tgaagccgcc 420 ggcggcatac cgatgctgaa atcccttggc ggccccttgc cgcaagtcac cttctgtccg 480 accggcggcg tcaatcccaa aaacgcgccc gaatatctgg cattgaaaaa tgtcgcctgc 540 gtcggcggct cctggatggc gccggccgat ctggtagatg ccgaagactg ggcggaaatc 600 acgcggcggg cgagcgaggc cgcggcattg aaaaaa 636 10 212 PRT METHYLOMONAS SP. 10 Glu Asn Thr Met Ser Val Thr Ile Lys Glu Val Met Thr Thr Ser Pro 1 5 10 15 Val Met Pro Val Met Val Ile Asn His Leu Glu His Ala Val Pro Leu 20 25 30 Ala Arg Ala Leu Val Asp Gly Gly Leu Lys Val Leu Glu Ile Thr Leu 35 40 45 Arg Thr Pro Val Ala Leu Glu Cys Ile Arg Arg Ile Lys Ala Glu Val 50 55 60 Pro Asp Ala Ile Val Gly Ala Gly Thr Ile Ile Asn Pro His Thr Leu 65 70 75 80 Tyr Gln Ala Ile Asp Ala Gly Ala Glu Phe Ile Val Ser Pro Gly Ile 85 90 95 Thr Glu Asn Leu Leu Asn Glu Ala Leu Ala Ser Gly Val Pro Ile Leu 100 105 110 Pro Gly Val Ile Thr Pro Ser Glu Val Met Arg Leu Leu Glu Lys Gly 115 120 125 Ile Asn Ala Met Lys Phe Phe Pro Ala Glu Ala Ala Gly Gly Ile Pro 130 135 140 Met Leu Lys Ser Leu Gly Gly Pro Leu Pro Gln Val Thr Phe Cys Pro 145 150 155 160 Thr Gly Gly Val Asn Pro Lys Asn Ala Pro Glu Tyr Leu Ala Leu Lys 165 170 175 Asn Val Ala Cys Val Gly Gly Ser Trp Met ala Pro Ala Asp Leu Val 180 185 190 Asp Ala Glu Asp Trp Ala Glu Ile Thr Arg Arg Ala Ser Glu Ala Ala 195 200 205 Ala Leu Lys Lys 210 11 1434 DNA METHYLOMONAS SP. 11 aacatgcaaa taaaaaccta taagaccaca ccctatgatg atcaaaaacc cggcacatcc 60 gggctaagaa aaaaggttaa agtttttcag caatccggct atctggaaaa tttcgttcag 120 tccattttca atagtttaga agattttcag ggaaaaattc tagttttagg cggcgacggc 180 cgatatttta atcgacaagc gattcagatc atcatcaaaa tggcggccgc taacgggttt 240 ggtgagctga tcatcggcca gggcggtctg ttgtcgacac cggcggcctc caatgtcatc 300 cgcaaatatc gcgctttcgg cggcatcatt ctatccgcca gccacaatcc cggtggtccc 360 gacgaagact tcggcatcaa atataacgtc ggcaatggcg ggccggcacc ggaaaagttc 420 accgacgcct tgttcgaaaa cagcaaaacc atcaccagct atcagatggc cgaaatcgac 480 gacatcgatc tcgatagcgt cggcgacgtc caaatcgatg gcataacaat ccgcatcatc 540 gatcccgtgg ccgattacgc cgaattgatg gcccggattt tcgatttcga cctgatcaag 600 caaagcatcg ccgccggctt gattaccttg cgcttcgacg cgatgcatgc cattaccggc 660 ccctatgcca aacatatact cgaagacgtg ctgggcgccg cgcccggttc ggtattcaac 720 gccgtaccgc tggaagactt cggcggcggc catcccgatc ccaacatggc gcacgcgcac 780 gagctcaccg aaatcatgtt cgggccgaat ccgccggttt tcggcgcggc ctcggacggt 840 gacggcgacc gcaacatgat catgggcgcc aatattttcg tcacccccag cgacagtctg 900 gccatcatgg cggccaacgc gcaattgatt cccgcctatg ccaagggcat tagcggcgtc 960 gcccgctcga tgccgaccag ccaggcggtc gacagggtcg cggataaatt gagtctgccg 1020 tgctacgaaa cgccgaccgg ctggaaattc tttggcaatt tgctggatgc cgacaaaatc 1080 acgctgtgcg gcgaagaaag cttcggttcc ggttccaatc atgtccggga aaaagacggc 1140 ttgtgggccg ttttattttg gctgaatttg cttgcgcgca agcgtcaacc ggccgaggat 1200 atcgtgcgtg aacattggca aaaatacggc cgcgacatct attgccgcca tgattacgaa 1260 gccgtcgatg ccgacatcgc caacggcatc gtagagcagc tgcgaaacca attgccgagc 1320 ttgcccggca aaacctgggg cgattacagc gtcaaattcg ccgacgaatt cagctatacc 1380 gatccggtcg atggtagcgt cagcagcaac caaggcatcc gcgtcggttt cgcc 1434 12 545 PRT METHYLOMONAS SP. 12 Asn Met Gln Ile Lys Thr Tyr Lys Thr Thr Pro Tyr Asp Asp Gln Lys 1 5 10 15 Pro Gly Thr Ser Gly Leu Arg Lys Lys Val Lys Val Phe Gln Gln Ser 20 25 30 Gly Tyr Leu Glu Asn Phe Val Gln Ser Ile Phe Asn Ser Leu Glu Asp 35 40 45 Phe Gln Gly Lys Ile Leu Val Leu Gly Gly Asp Gly Arg Tyr Phe Asn 50 55 60 Arg Gln Ala Ile Gln Ile Ile Ile Lys Met ala Ala Ala Asn Gly Phe 65 70 75 80 Gly Glu Leu Ile Ile Gly Gln Gly Gly Leu Leu Ser Thr Pro Ala Ala 85 90 95 Ser Asn Val Ile Arg Lys Tyr Arg Ala Phe Gly Gly Ile Ile Leu Ser 100 105 110 Ala Ser His Asn Pro Gly Gly Pro Asp Glu Asp Phe Gly Ile Lys Tyr 115 120 125 Asn Val Gly Asn Gly Gly Pro Ala Pro Glu Lys Phe Thr Asp Ala Leu 130 135 140 Phe Glu Asn Ser Lys Thr Ile Thr Ser Tyr Gln Met ala Glu Ile Asp 145 150 155 160 Asp Ile Asp Leu Asp Ser Val Gly Asp Val Gln Ile Asp Gly Ile Thr 165 170 175 Ile Arg Ile Ile Asp Pro Val Ala Asp Tyr Ala Glu Leu Met ala Arg 180 185 190 Ile Phe Asp Phe Asp Leu Ile Lys Gln Ser Ile Ala Ala Gly Leu Ile 195 200 205 Thr Leu Arg Phe Asp Ala Met His Ala Ile Thr Gly Pro Tyr Ala Lys 210 215 220 His Ile Leu Glu Asp Val Leu Gly Ala Ala Pro Gly Ser Val Phe Asn 225 230 235 240 Ala Val Pro Leu Glu Asp Phe Gly Gly Gly His Pro Asp Pro Asn Met 245 250 255 Ala His Ala His Glu Leu Thr Glu Ile Met Phe Gly Pro Asn Pro Pro 260 265 270 Val Phe Gly Ala Ala Ser Asp Gly Asp Gly Asp Arg Asn Met Ile Met 275 280 285 Gly Ala Asn Ile Phe Val Thr Pro Ser Asp Ser Leu Ala Ile Met ala 290 295 300 Ala Asn Ala Gln Leu Ile Pro Ala Tyr Ala Lys Gly Ile Ser Gly Val 305 310 315 320 Ala Arg Ser Met Pro Thr Ser Gln Ala Val Asp Arg Val Ala Asp Lys 325 330 335 Leu Ser Leu Pro Cys Tyr Glu Thr Pro Thr Gly Trp Lys Phe Phe Gly 340 345 350 Asn Leu Leu Asp Ala Asp Lys Ile Thr Leu Cys Gly Glu Glu Ser Phe 355 360 365 Gly Ser Gly Ser Asn His Val Arg Glu Lys Asp Gly Leu Trp Ala Val 370 375 380 Leu Phe Trp Leu Asn Leu Leu Ala Arg Lys Arg Gln Pro Ala Glu Asp 385 390 395 400 Ile Val Arg Glu His Trp Gln Lys Tyr Gly Arg Asp Ile Tyr Cys Arg 405 410 415 His Asp Tyr Glu Ala Val Asp Ala Asp Ile Ala Asn Gly Ile Val Glu 420 425 430 Gln Leu Arg Asn Gln Leu Pro Ser Leu Pro Gly Lys Thr Trp Gly Asp 435 440 445 Tyr Ser Val Lys Phe Ala Asp Glu Phe Ser Tyr Thr Asp Pro Val Asp 450 455 460 Gly Ser Val Ser Ser Asn Gln Gly Ile Arg Val Gly Phe Ala Asn Gly 465 470 475 480 Ser Arg Ile Val Phe Arg Leu Ser Gly Thr Gly Thr Val Gly Ala Thr 485 490 495 Leu Arg Ile Tyr Leu Glu Arg Tyr Glu Arg Asp Val Arg Asn His Asp 500 505 510 Gln Asp Pro Gln Val Ala Leu Ala Glu Leu Ile Glu Ile Ala Glu Gln 515 520 525 Leu Cys Gln Val Lys Gln Arg Thr Gly Arg Thr Glu Pro Ser Val Ile 530 535 540 Thr 545 13 1387 DNA METHYLOMONAS SP. 13 ccgaaagcag gcaaaatcac ggttcatttt tttttgtcat ccgtcaaaga caatccttat 60 aatgaggtaa tcgttctcct cgctacatct ggcactaaag cttccgaaga ctctttatcc 120 ggttcacaca aaaataatat gtccaaatta atcaactctg ccgaatggaa cgccgtcaaa 180 caacatcatc aagaaattgc tggtaaattt tgcatgaaag aggcttttgc caaagatccc 240 cagcgtttcg ataaattctc cgtcaccttt aacgacatat tattagacta ttccaaaaac 300 ctgatcgacg agcgcaccat gcccttgctg atcgcattgg caaagcgggc agacttgcgc 360 gagaaaacgg aagcgatgtt ttccggctcc atcatcaaca ccaccgaaaa acgcgcggtt 420 ttgcataccg cgctgcgaaa ccgtagcaat acgcccgttt tcttccgcgg ccaggatgtc 480 atgccggaaa tcaacaaggt tctggcaaaa atgcgggttt tcgtggaaca ggtgcgttcg 540 ggccaatgga cgggctatag cggcaaggcc attaccgata tcgtcaacat cggcattggc 600 ggctcggatc tcggcccgaa aatggtcgac accgccttga cgccgtacgg caaaaacggc 660 ttaaaagcgc atttcgtatc caatgtcgat caaaccgaca tcgtcgaaac cctgaaaccg 720 ctcaatccgg aaaccacgct gttcctgatt tcatcgaaaa cgtttaccac gcaggaaacc 780 atgaccaatg cgcgctcggc acgtaactgg ttcatgaatg ccgcgcaaga tcccgcccat 840 atcaagaaac atttcatcgc catttccacc aacgaagaaa tggtcaagga attcggcatc 900 gacccggcga acatgttcga gttctgggac tgggtcggcg ggcgttattc gctctggtcg 960 gtcatcggca tgtcgatagc tttatatatc ggcatggaca atttcgaaga actgctgatg 1020 ggtgcgcact tggccgacga acatttccgc catgcgccct acgaggaaaa cattccggtc 1080 atcatgggct tgctcggcat ctggtacaac aacttcttcg aagcggaaac ctatgccatt 1140 ttgccgtatg cgcaatcctt gaaatatttt gccgattatt tccagcaagg cgacatggaa 1200 agcaacggca aaagcgcgac gatcaccggt gaaaaagtcg attacaacac gggccccatc 1260 atctggggac agcccggcac caatggtcag cacgccttct ttcaattgat tcaccaaggc 1320 accaaactgg ttcccggcga ttttctggcg gccgcgcaaa gtcagtatga tttaccggat 1380 caccacg 1387 14 592 PRT METHYLOMONAS SP. 14 Pro Lys Ala Gly Lys Ile Thr Val His Phe Phe Leu Ser Ser Val Lys 1 5 10 15 Asp Asn Pro Tyr Asn Glu Val Ile Val Leu Leu Ala Thr Ser Gly Thr 20 25 30 Lys Ala Ser Glu Asp Ser Leu Ser Gly Ser His Lys Asn Asn Met Ser 35 40 45 Lys Leu Ile Asn Ser Ala Glu Trp Asn Ala Val Lys Gln His His Gln 50 55 60 Glu Ile Ala Gly Lys Phe Cys Met Lys Glu Ala Phe Ala Lys Asp Pro 65 70 75 80 Gln Arg Phe Asp Lys Phe Ser Val Thr Phe Asn Asp Ile Leu Leu Asp 85 90 95 Tyr Ser Lys Asn Leu Ile Asp Glu Arg Thr Met Pro Leu Leu Ile Ala 100 105 110 Leu Ala Lys Arg Ala Asp Leu Arg Glu Lys Thr Glu Ala Met Phe Ser 115 120 125 Gly Ser Ile Ile Asn Thr Thr Glu Lys Arg Ala Val Leu His Thr Ala 130 135 140 Leu Arg Asn Arg Ser Asn Thr Pro Val Phe Phe Arg Gly Gln Asp Val 145 150 155 160 Met Pro Glu Ile Asn Lys Val Leu Ala Lys Met Arg Val Phe Val Glu 165 170 175 Gln Val Arg Ser Gly Gln Trp Thr Gly Tyr Ser Gly Lys Ala Ile Thr 180 185 190 Asp Ile Val Asn Ile Gly Ile Gly Gly Ser Asp Leu Gly Pro Lys Met 195 200 205 Val Asp Thr Ala Leu Thr Pro Tyr Gly Lys Asn Gly Leu Lys Ala His 210 215 220 Phe Val Ser Asn Val Asp Gln Thr Asp Ile Val Glu Thr Leu Lys Pro 225 230 235 240 Leu Asn Pro Glu Thr Thr Leu Phe Leu Ile Ser Ser Lys Thr Phe Thr 245 250 255 Thr Gln Glu Thr Met Thr Asn Ala Arg Ser Ala Arg Asn Trp Phe Met 260 265 270 Asn Ala Ala Gln Asp Pro Ala His Ile Lys Lys His Phe Ile Ala Ile 275 280 285 Ser Thr Asn Glu Glu Met Val Lys Glu Phe Gly Ile Asp Pro Ala Asn 290 295 300 Met Phe Glu Phe Trp Asp Trp Val Gly Gly Arg Tyr Ser Leu Trp Ser 305 310 315 320 Val Ile Gly Met Ser Ile Ala Leu Tyr Ile Gly Met Asp Asn Phe Glu 325 330 335 Glu Leu Leu Met Gly Ala His Leu Ala Asp Glu His Phe Arg His Ala 340 345 350 Pro Tyr Glu Glu Asn Ile Pro Val Ile Met Gly Leu Leu Gly Ile Trp 355 360 365 Tyr Asn Asn Phe Phe Glu Ala Glu Thr Tyr Ala Ile Leu Pro Tyr Ala 370 375 380 Gln Ser Leu Lys Tyr Phe Ala Asp Tyr Phe Gln Gln Gly Asp Met Glu 385 390 395 400 Ser Asn Gly Lys Ser Ala Thr Ile Thr Gly Glu Lys Val Asp Tyr Asn 405 410 415 Thr Gly Pro Ile Ile Trp Gly Gln Pro Gly Thr Asn Gly Gln His Ala 420 425 430 Phe Phe Gln Leu Ile His Gln Gly Thr Lys Leu Val Pro Gly Asp Phe 435 440 445 Leu Ala Ala Ala Gln Ser Gln Tyr Asp Leu Pro Asp His His Asp Ile 450 455 460 Leu Ile Ser Asn Phe Leu Ala Gln Ala Glu Ala Leu Met Arg Gly Lys 465 470 475 480 Thr Glu Glu Glu Val Arg Gln Asp Leu Ser His Glu Pro Asn Leu Asp 485 490 495 Asp Ala Leu Ile Ala Ser Lys Ile Phe Glu Gly Asn Lys Pro Ser Asn 500 505 510 Ser Phe Leu Phe Lys Lys Leu Thr Pro Arg Thr Leu Gly Thr Leu Ile 515 520 525 Ala Phe Tyr Glu His Lys Ile Phe Val Gln Gly Val Ile Trp Asn Ile 530 535 540 Asn Ser Phe Asp Gln Met Gly Val Glu Leu Gly Lys Val Leu Ala Lys 545 550 555 560 Ala Ile Leu Pro Glu Leu Lys Asn Asp Asp Ile Ile Ala Ser His Asp 565 570 575 Ser Ser Thr Asn Gly Leu Ile Asn Thr Tyr Lys Arg Leu Arg Lys Ala 580 585 590 15 1311 DNA METHYLOMONAS SP. 15 gatgtggtca catggcccta tcacttaacg gctgatattc gattttgtca ttggtttttt 60 cttaacttta acttctacac gctcatgaac aaacctaaaa aagttgcaat actgacagca 120 ggcggcttgg cgccttgttt gaattccgca atcggtagtt tgatcgaacg ttataccgaa 180 atcgatccta gcatagaaat catttgctat cgcggcggtt ataaaggcct gttgctgggc 240 gattcttatc cagtaacggc cgaagtgcgt aaaaaggcgg gtgttctgca acgttttggc 300 ggttctgtga tcggcaacag ccgcgtcaaa ttgaccaatg tcaaagactg cgtgaaacgc 360 ggtttggtca aagagggtga agatccgcaa aaagtcgcgg ctgatcaatt ggttaaggat 420 ggtgtcgata ttctgcacac catcggcggc gatgatacca atacggcagc agcggatttg 480 gcagcattcc tggccagaaa taattacgga ctgaccgtca ttggtttacc taaaaccgtc 540 gataacgacg tatttccgat caagcaatca ctaggtgctt ggactgccgc cgagcaaggc 600 gcgcgttatt tcatgaacgt ggtggccgaa aacaacgcca acccacgcat gctgatcgta 660 cacgaagtga tgggccgtaa ctgcggctgg ctgaccgctg caaccgcgca ggaatatcgc 720 aaattactgg accgtgccga gtggttgccg gaattgggtt tgactcgtga atcttatgaa 780 gtgcacgcgg tattcgttcc ggaaatggcg atcgacctgg aagccgaagc caagcgcctg 840 cgcgaagtga tggacaaagt cgattgcgtc aacatcttcg tttccgaagg tgccggcgtc 900 gaagctatcg tcgcggaaat gcaggccaaa ggccaggaag tgccgcgcga tgcgttcggc 960 cacatcaaac tggatgcggt caaccctggt aaatggttcg gcgagcaatt cgcgcagatg 1020 ataggcgcgg aaaaaaccct ggtacaaaaa tcgggatact tcgcccgtgc ttctgcttcc 1080 aacgttgacg acatgcgttt gatcaaatcg tgcgccgact tggcggtcga gtgcgcgttc 1140 cgccgcgagt ctggcgtgat cggtcacgac gaagacaacg gcaacgtgtt gcgtgcgatc 1200 gagtttccgc gcatcaaggg cggcaaaccg ttcaatatcg acaccgactg gttcaatagc 1260 atgttgagcg aaatcggcca gcctaaaggc ggtaaagtcg aagtcagcca c 1311 16 437 PRT METHYLOMONAS SP. 16 Asp Val Val Thr Trp Pro Tyr His Leu Thr Ala Asp Ile Arg Phe Cys 1 5 10 15 His Trp Phe Phe Leu Asn Phe Asn Phe Tyr Thr Leu Met Asn Lys Pro 20 25 30 Lys Lys Val Ala Ile Leu Thr Ala Gly Gly Leu Ala Pro Cys Leu Asn 35 40 45 Ser Ala Ile Gly Ser Leu Ile Glu Arg Tyr Thr Glu Ile Asp Pro Ser 50 55 60 Ile Glu Ile Ile Cys Tyr Arg Gly Gly Tyr Lys Gly Leu Leu Leu Gly 65 70 75 80 Asp Ser Tyr Pro Val Thr Ala Glu Val Arg Lys Lys Ala Gly Val Leu 85 90 95 Gln Arg Phe Gly Gly Ser Val Ile Gly Asn Ser Arg Val Lys Leu Thr 100 105 110 Asn Val Lys Asp Cys Val Lys Arg Gly Leu Val Lys Glu Gly Glu Asp 115 120 125 Pro Gln Lys Val Ala Ala Asp Gln Leu Val Lys Asp Gly Val Asp Ile 130 135 140 Leu His Thr Ile Gly Gly Asp Asp Thr Asn Thr Ala Ala Ala Asp Leu 145 150 155 160 Ala Ala Phe Leu Ala Arg Asn Asn Tyr Gly Leu Thr Val Ile Gly Leu 165 170 175 Pro Lys Thr Val Asp Asn Asp Val Phe Pro Ile Lys Gln Ser Leu Gly 180 185 190 Ala Trp Thr Ala Ala Glu Gln Gly Ala Arg Tyr Phe Met Asn Val Val 195 200 205 Ala Glu Asn Asn Ala Asn Pro Arg Met Leu Ile Val His Glu Val Met 210 215 220 Gly Arg Asn Cys Gly Trp Leu Thr Ala Ala Thr Ala Gln Glu Tyr Arg 225 230 235 240 Lys Leu Leu Asp Arg Ala Glu Trp Leu Pro Glu Leu Gly Leu Thr Arg 245 250 255 Glu Ser Tyr Glu Val His Ala Val Phe Val Pro Glu Met ala Ile Asp 260 265 270 Leu Glu Ala Glu Ala Lys Arg Leu Arg Glu Val Met Asp Lys Val Asp 275 280 285 Cys Val Asn Ile Phe Val Ser Glu Gly Ala Gly Val Glu Ala Ile Val 290 295 300 Ala Glu Met Gln Ala Lys Gly Gln Glu Val Pro Arg Asp Ala Phe Gly 305 310 315 320 His Ile Lys Leu Asp Ala Val Asn Pro Gly Lys Trp Phe Gly Glu Gln 325 330 335 Phe Ala Gln Met Ile Gly Ala Glu Lys Thr Leu Val Gln Lys Ser Gly 340 345 350 Tyr Phe Ala Arg Ala Ser Ala Ser Asn Val Asp Asp Met Arg Leu Ile 355 360 365 Lys Ser Cys Ala Asp Leu Ala Val Glu Cys Ala Phe Arg Arg Glu Ser 370 375 380 Gly Val Ile Gly His Asp Glu Asp Asn Gly Asn Val Leu Arg Ala Ile 385 390 395 400 Glu Phe Pro Arg Ile Lys Gly Gly Lys Pro Phe Asn Ile Asp Thr Asp 405 410 415 Trp Phe Asn Ser Met Leu Ser Glu Ile Gly Gln Pro Lys Gly Gly Lys 420 425 430 Val Glu Val Ser His 435 17 1360 DNA METHYLOMONAS SP. 17 agtgtcccgc actcgcatca cccggagaca tccttaatgc atcccgtact cgaaaaagtc 60 acagaacaag tcatcgcccg cagccgggaa acccgtgccg cttatctgaa gcgcatagag 120 gccgccatcg ccgaaggccc gcaacgcaat aaactgcctt gcgccaatct ggcccacggt 180 ttcgcggtct gttcggccat cgaaaaagaa gaattgtctc atggccccaa gcccaatgtc 240 ggcatcatct cggcctacaa cgacatgctg tccgcgcacg aaccctacaa ggattatcct 300 gccctgatca aacaggccgt gcgcgaagcc ggcggcgtgg ctcaattcgc cggcggcgtg 360 cccgcgatgt gcgacggcgt cacccagggc atgccgggca tggaattgtc gctattcagc 420 cgcgacgtca tcgcgatgtc caccgcgatc ggcctggctc ataacatgtt cgacgcggcg 480 ctgtatctgg gcgtctgcga caagatcgta cccggtttgt tgatcggtgc attgagcttc 540 ggccatttgc cggccgtttt cttgccagcc ggccccatga ccagcggcct gtccaacaag 600 gaaaaatccc gtgcccggca aaaatacgcc gaaggtaaga tcggtgaaaa agaattgctg 660 gaatcggaag ccaagtctta ccacagccca ggcacctgca ccttctatgg caccgccaac 720 agcaaccaga tgatggtcga gatcatgggc ctgcacctgc ccggtagttc cttcatcaat 780 ccttacaccc cactgcgcga cgaactgacc aaggccgccg ccaggcaggt gttgaaattc 840 accgcgctgg gcaacgactt caggccaatc gcgcatgtga tcgacgaaaa agccatcatc 900 aatgccatca tcggcttgct ggcgaccggc ggttcgacca accataccat ccatttgatc 960 gcgattgccc gcgccgccgg catcatcatc aactgggacg atttcgacgc cctatccaaa 1020 gtcattccgt tgctgaccaa gatctatccg aacggcccgg ccgacgtcaa ccaattccag 1080 gcggccggcg gcatgagctt attgatacac gaactgctgg atcacggctt gttgcacggc 1140 gacatcctga ccataggcga ccagcgcggc atggcccaat acagtcaagt accgacgctg 1200 caagacggcc aattacaatg gcagcccggt cctaccgcat cgcgcgatcc cgaaatcatc 1260 gccagcgtgg caaaaccttt cgccgccggt ggtggcctgc atgtgatgca tggcaatctg 1320 ggccgcggcg tatccaagat ttccgccgtc tccgaagatc 1360 18 618 PRT METHYLOMONAS SP. 18 Ser Val Pro His Ser His His Pro Glu Thr Ser Leu Met His Pro Val 1 5 10 15 Leu Glu Lys Val Thr Glu Gln Val Ile Ala Arg Ser Arg Glu Thr Arg 20 25 30 Ala Ala Tyr Leu Lys Arg Ile Glu Ala Ala Ile Ala Glu Gly Pro Gln 35 40 45 Arg Asn Lys Leu Pro Cys Ala Asn Leu Ala His Gly Phe Ala Val Cys 50 55 60 Ser Ala Ile Glu Lys Glu Glu Leu Ser His Gly Pro Lys Pro Asn Val 65 70 75 80 Gly Ile Ile Ser Ala Tyr Asn Asp Met Leu Ser Ala His Glu Pro Tyr 85 90 95 Lys Asp Tyr Pro Ala Leu Ile Lys Gln Ala Val Arg Glu Ala Gly Gly 100 105 110 Val Ala Gln Phe Ala Gly Gly Val Pro Ala Met Cys Asp Gly Val Thr 115 120 125 Gln Gly Met Pro Gly Met Glu Leu Ser Leu Phe Ser Arg Asp Val Ile 130 135 140 Ala Met Ser Thr Ala Ile Gly Leu Ala His Asn Met Phe Asp Ala Ala 145 150 155 160 Leu Tyr Leu Gly Val Cys Asp Lys Ile Val Pro Gly Leu Leu Ile Gly 165 170 175 Ala Leu Ser Phe Gly His Leu Pro Ala Val Phe Leu Pro Ala Gly Pro 180 185 190 Met Thr Ser Gly Leu Ser Asn Lys Glu Lys Ser Arg Ala Arg Gln Lys 195 200 205 Tyr Ala Glu Gly Lys Ile Gly Glu Lys Glu Leu Leu Glu Ser Glu Ala 210 215 220 Lys Ser Tyr His Ser Pro Gly Thr Cys Thr Phe Tyr Gly Thr Ala Asn 225 230 235 240 Ser Asn Gln Met Met Val Glu Ile Met Gly Leu His Leu Pro Gly Ser 245 250 255 Ser Phe Ile Asn Pro Tyr Thr Pro Leu Arg Asp Glu Leu Thr Lys Ala 260 265 270 Ala Ala Arg Gln Val Leu Lys Phe Thr Ala Leu Gly Asn Asp Phe Arg 275 280 285 Pro Ile Ala His Val Ile Asp Glu Lys Ala Ile Ile Asn Ala Ile Ile 290 295 300 Gly Leu Leu Ala Thr Gly Gly Ser Thr Asn His Thr Ile His Leu Ile 305 310 315 320 Ala Ile Ala Arg Ala Ala Gly Ile Ile Ile Asn Trp Asp Asp Phe Asp 325 330 335 Ala Leu Ser Lys Val Ile Pro Leu Leu Thr Lys Ile Tyr Pro Asn Gly 340 345 350 Pro Ala Asp Val Asn Gln Phe Gln Ala Ala Gly Gly Met Ser Leu Leu 355 360 365 Ile His Glu Leu Leu Asp His Gly Leu Leu His Gly Asp Ile Leu Thr 370 375 380 Ile Gly Asp Gln Arg Gly Met ala Gln Tyr Ser Gln Val Pro Thr Leu 385 390 395 400 Gln Asp Gly Gln Leu Gln Trp Gln Pro Gly Pro Thr Ala Ser Arg Asp 405 410 415 Pro Glu Ile Ile Ala Ser Val Ala Lys Pro Phe Ala Ala Gly Gly Gly 420 425 430 Leu His Val Met His Gly Asn Leu Gly Arg Gly Val Ser Lys Ile Ser 435 440 445 Ala Val Ser Glu Asp His Gln Val Val Thr Ala Pro Ala Met Val Phe 450 455 460 Asp Asp Gln Leu Asp Val Val Ala Ala Phe Lys Arg Gly Glu Leu Glu 465 470 475 480 Lys Asp Val Ile Val Val Leu Arg Phe Gln Gly Pro Lys Ala Asn Gly 485 490 495 Met Pro Glu Leu His Lys Leu Thr Pro Val Leu Gly Val Leu Gln Asp 500 505 510 Arg Gly Phe Lys Val Gly Leu Leu Thr Asp Gly Arg Met Ser Gly Ala 515 520 525 Ser Gly Lys Val Pro Ser Ala Ile His Met Trp Pro Glu Cys Ile Asp 530 535 540 Gly Gly Pro Leu Ala Lys Val Arg Asp Gly Asp Ile Ile Val Met Asn 545 550 555 560 Thr Gln Thr Gly Glu Val Asn Val Gln Val Asp Pro Ala Glu Phe Lys 565 570 575 Ala Arg Val Ala Glu Pro Asn His Ala Thr Gly His His Phe Gly Met 580 585 590 Gly Arg Glu Leu Phe Gly Ala Met Arg Ala Gln Ala Ser Thr Ala Glu 595 600 605 Thr Gly Ala Thr Asn Leu Phe Phe Val Asp 610 615 19 1477 DNA METHYLOMONAS SP. 19 atggcattgg gctttttgct ccgtagcccc aaagacatga caaaaaacat tacttacaaa 60 ccctgcgacc tggtgattta cggcgcactg ggcgatttat ccaaacgtaa actactgatt 120 tcattatacc gtttggaaaa acacaatctg ctcgagcccg atacgcgcat catcggcgta 180 gatcgtttgg aagaaaccag cgacagtttc gtcgaaattg cgcacaaaag cttgcaggcg 240 tttttgaaca acgtcatcga cgcagaaatc tggcaacgtt tttccaaacg cttgtcctat 300 ttgaaaatcg atctgaccca acccgagcaa tacaaacaac tgcatacggt cgtcgatgcc 360 gaaaaacgag tcatggtgaa ttatttcgcg gtggcaccct ttttgttcaa aaacatttgc 420 caaggcttgc atgactgcgg cgtattgacg gccgaatcgc gcatggtgat ggaaaaaccc 480 atcggccacg acctgaaatc gtcgaaagaa atcaacgacg tcgtcgccga cgtattccac 540 gaagaccagg tctaccgcat cgaccactac ctgggcaagg aaacggtctt gaacttgctg 600 gccttgcgtt tcgccaattc gatattcacg accaactgga atcacaacac gatagaccat 660 atccagatta cggtcggtga ggacatcggc atcgagggcc gttgggaata tttcgacaag 720 accggccaat tgcgcgacat gctgcaaaac catttgctgc aaatcctgac cttcgtcgcg 780 atggagccgc ccgcggatct gtcggccgaa agcatacaca tggaaaaaat caaggtcctg 840 aaagccttgc ggccaatcac cgtgcgcaat gtcgaggaaa aaaccgtgcg cggtcaatac 900 accgccggtt tcatcaaagg caagtcggta ccgggttatc tggaagaaga aggtgccaac 960 accgaaagca cgaccgaaac tttcgtcgcg atccgcgtgg atatcgataa ctggcgctgg 1020 gccggtgtcc cgttttacat gcgtaccggc aaacgcacgc ccaacaaacg caccgagatt 1080 gtggtcaatt tcaagcaatt gccgcacaac atcttcaagg acagttttca tgaactgccg 1140 gccaataaac tggtcattca tttgcaaccg aacgaagggg tggatgtcat gatgttgaac 1200 aaggtgccgg gcatagacgg caacatcaag ttgcaacaga ccaaactgga tttgagcttt 1260 tccgaaacct tcaagaaaaa ccgaattttc ggcggctacg aaaaactgat tctggaagcc 1320 ctgcgcggca acccgacgct gtttttgagc cgcgaggaaa tagaacaagc ctggacctgg 1380 gtcgattcga ttcaggatgc ctggcaacac aaccacacgc cacccaaacc ctatcccgcg 1440 ggtagctggg gtccagtggc atcggtcgca ttactgg 1477 20 501 PRT METHYLOMONAS SP. 20 Met ala Leu Gly Phe Leu Leu Arg Ser Pro Lys Asp Met Thr Lys Asn 1 5 10 15 Ile Thr Tyr Lys Pro Cys Asp Leu Val Ile Tyr Gly Ala Leu Gly Asp 20 25 30 Leu Ser Lys Arg Lys Leu Leu Ile Ser Leu Tyr Arg Leu Glu Lys His 35 40 45 Asn Leu Leu Glu Pro Asp Thr Arg Ile Ile Gly Val Asp Arg Leu Glu 50 55 60 Glu Thr Ser Asp Ser Phe Val Glu Ile Ala His Lys Ser Leu Gln Ala 65 70 75 80 Phe Leu Asn Asn Val Ile Asp Ala Glu Ile Trp Gln Arg Phe Ser Lys 85 90 95 Arg Leu Ser Tyr Leu Lys Ile Asp Leu Thr Gln Pro Glu Gln Tyr Lys 100 105 110 Gln Leu His Thr Val Val Asp Ala Glu Lys Arg Val Met Val Asn Tyr 115 120 125 Phe Ala Val Ala Pro Phe Leu Phe Lys Asn Ile Cys Gln Gly Leu His 130 135 140 Asp Cys Gly Val Leu Thr Ala Glu Ser Arg Met Val Met Glu Lys Pro 145 150 155 160 Ile Gly His Asp Leu Lys Ser Ser Lys Glu Ile Asn Asp Val Val Ala 165 170 175 Asp Val Phe His Glu Asp Gln Val Tyr Arg Ile Asp His Tyr Leu Gly 180 185 190 Lys Glu Thr Val Leu Asn Leu Leu Ala Leu Arg Phe Ala Asn Ser Ile 195 200 205 Phe Thr Thr Asn Trp Asn His Asn Thr Ile Asp His Ile Gln Ile Thr 210 215 220 Val Gly Glu Asp Ile Gly Ile Glu Gly Arg Trp Glu Tyr Phe Asp Lys 225 230 235 240 Thr Gly Gln Leu Arg Asp Met Leu Gln Asn His Leu Leu Gln Ile Leu 245 250 255 Thr Phe Val Ala Met Glu Pro Pro Ala Asp Leu Ser Ala Glu Ser Ile 260 265 270 His Met Glu Lys Ile Lys Val Leu Lys Ala Leu Arg Pro Ile Thr Val 275 280 285 Arg Asn Val Glu Glu Lys Thr Val Arg Gly Gln Tyr Thr Ala Gly Phe 290 295 300 Ile Lys Gly Lys Ser Val Pro Gly Tyr Leu Glu Glu Glu Gly Ala Asn 305 310 315 320 Thr Glu Ser Thr Thr Glu Thr Phe Val Ala Ile Arg Val Asp Ile Asp 325 330 335 Asn Trp Arg Trp Ala Gly Val Pro Phe Tyr Met Arg Thr Gly Lys Arg 340 345 350 Thr Pro Asn Lys Arg Thr Glu Ile Val Val Asn Phe Lys Gln Leu Pro 355 360 365 His Asn Ile Phe Lys Asp Ser Phe His Glu Leu Pro Ala Asn Lys Leu 370 375 380 Val Ile His Leu Gln Pro Asn Glu Gly Val Asp Val Met Met Leu Asn 385 390 395 400 Lys Val Pro Gly Ile Asp Gly Asn Ile Lys Leu Gln Gln Thr Lys Leu 405 410 415 Asp Leu Ser Phe Ser Glu Thr Phe Lys Lys Asn Arg Ile Phe Gly Gly 420 425 430 Tyr Glu Lys Leu Ile Leu Glu Ala Leu Arg Gly Asn Pro Thr Leu Phe 435 440 445 Leu Ser Arg Glu Glu Ile Glu Gln Ala Trp Thr Trp Val Asp Ser Ile 450 455 460 Gln Asp Ala Trp Gln His Asn His Thr Pro Pro Lys Pro Tyr Pro Ala 465 470 475 480 Gly Ser Trp Gly Pro Val Ala Ser Val Ala Leu Leu Ala Arg Asp Gly 485 490 495 Arg Ala Trp Glu Glu 500 

What is claimed is:
 1. A method of altering carbon flow through a methanotrophic bacteria comprising, over-expressing a phosphofructokinase gene as set fourth in SEQ ID NO: 15 in a methanotrophic strain such that the carbon flow is altered through the strain.
 2. A metod according to claim 1 wherein said methanotrophic bacteria: (a) grows on a C1 carbon substrate selected from the group consisting of methane and methanol; and (b) comprises a functional Embden-Meyerhof carbon pathway, said pathway comprising a gene encoding a pyrophosphate dependent phosphofructokinase enzyme.
 3. A method according to claim 2 wherein said methanotrophic bacteria is Methylomonas 16a ATCC PTA
 2402. 4. A method according to claim 1 wherein said phosphofructokinase gene is over-expressed on a multicopy plasmid.
 5. A method according to claim 1 wherein said phosphofructokinase gene is operably linked to an inducible regulated promoter. 